Stargate Atlantis  Season 6
by MeB XanWill4Ever
Summary: Season Five of Stargate Atlantis is over...but resumes in Season Six  Fiction .  Atlantis heads back to the Pegasus Galaxy to face the Wraith...and new challenges await them!
1. The Descended Ones Part 1

The Descended Ones (Part 1)

_ Prologue _

Something was wrong. It wasn't just the headache. He's had plenty of headaches before, so that clearly wasn't the problem. He felt a little odd, though. Like he had been floating in water, caught in a current. It was a feeling of disorientation.

_Damn!_ he thought. _I should'a had a V-8._

He tried to open his eyes, but they were heavy. Suddenly, he felt nauseous and thought that he just might throw up. Somehow, he didn't. He wouldn't lose his dignity by doing the unthinkable, especially if he was in a room with other people. He didn't hear anyone present with him but that didn't mean they weren't there.

He forced his eyes open...and there was the ceiling. It looked familiar to him. He was in a room he had been in before. He was also aware of things he normally would not be aware of, like the operations of the entire city and how it was moving...That was when Lt. Colonel John Sheppard realized exactly where he was. He was sitting in the Control Chair in Atlantis and no one else was in the room with him. The problem with that was he didn't know how he got there.

"What the hell...?" he said out loud. He swallowed as he tried to recall the events that led him to sitting in the Chair in the first place. _Was Atlantis really moving?_

The radio in his ear came to life. _"Sheppard!"_

It was Rodney McKay. Sheppard hoped he had some answers. "Rodney, what the hell is going on?"

_"Whatever you do, don't get out of the chair! We're in hyperspace and no one seems to know what happened, so if you make any sudden moves until we can figure out what happened, we'll not know where we are until we collide with a meteor or a planet! Or a sun! So just don't get up!"_

Sheppard frowned. "I have no intention of getting up. I think we're pretty much on cruise right now anyway, 'cause I can't tell where we are or where we're going." He stopped. "Crap. Weren't we on earth?"

_"Colonel Sheppard, it's Richard Woolsey." _A pause came over the radio. _"As far as we're able to determine, Atlantis is not only no longer on earth, but as Dr. McKay already told you, it's in hyperspace heading back to the Pegasus Galaxy."_

Sheppard let out an irritated sigh. "He told me we were in hyperspace," he confirmed, "but he didn't say anything about our heading! How did this happen?"

_"We're...not certain. We're still looking into it, and others are still regaining consciousness."_

"Regaining consciousness?"

_"Colonel Sheppard, we'll talk about it when we know more and when we can actually have a meeting about this. Right now, everyone who is conscious is doing their part to restore order. You need to remain in the Chair. Dr. McKay assures me that when we arrive at our destination, you're going to have to bring us in for a landing."_

"Come on. I should be able to get us out of hyperspace now, can't I? At least to see where we are."

_"That is a bad idea!"_ McKay snapped over the radio. _"I already told you about the dangers of jumping out of hyperspace when we have no idea where we are. Meteors, planets or even a sun could be right in our path. Trust me, Sheppard. There are other factors going on here that you don't know about yet and I haven't got time to go into them at the moment, so if you don't mind, I've got work to do."_

Sheppard sighed. "Well, can somebody tell me how long I've been in this Chair?"

_"Twenty-four hours, give or take,"_ Woolsey replied.

He whistled. "Son-of-a-bitch," he cursed. "No wonder I have a headache. I could use some coffee...and maybe a sandwich."

_"We'll get you out of that Chair momentarily, Colonel Sheppard. And you'll get that coffee as well."_

With nothing better to do, Sheppard sat back and stared up at the ceiling. "Wouldn't really need to get me out of this Chair if there were cup holders." He glanced at the arms of the Control Chair. "Cup holders would be nice."

There was no reply over the radio.

The briefing room was full, and Sheppard wasn't sure he liked it. Richard Woolsey was there at the head of the table, looking even more grim than he ever had. Rodney McKay was glaring at his laptop as if it had offended him. For all Sheppard knew, maybe it did. The man was brilliant, but he got awful cranky over the smallest things. Of course, the current situation was no small thing. Teyla Emmagan and Ronon Dex were seated quietly at the table, but Ronon had his eyes narrowed at a couple of newcomers who were crashing the party. They were from the International Oversight Advisory, otherwise known as the IOA, and as far as Sheppard was concerned, they weren't a welcome addition to the meeting. If anything, he expected them only to complicate matters fully.

Harris Johanson was the man who spoke for the IOA on Atlantis. He had already hinted at taking over Atlantis if Woolsey and he didn't see eye to eye. Sheppard didn't trust the man. Johanson had a military background and could hold his own, but he had some political clout to back him up, too. He was also the man that Ronon wouldn't stop glaring at. The woman with Johanson was Patricia Manor, and even though she was good to look at, Sheppard had already had one run in with her that made him want to toss her off the balcony. She was not nice, to put it mildly.

Radek Zelenka was also at the table, and he nodded a greeting to Sheppard as he took his seat. Sheppard wasn't sure what to expect at the meeting. He had been relieved by Dr. Carson Beckett - who was now in the Chair - and then grabbed some much needed coffee and a bite to eat. As he took his chair, he could feel the two IOA members glaring daggers at him. _What the hell did I do now?_ he thought.

"I think we've wasted enough time," Johanson snapped before anyone could bring themselves to speak. He cast a whithering glare in Ronon's direction before continuing. "This meeting shouldn't take long, Mr. Woolsey, because frankly there is only one option open to you right now. Stop Atlantis. Turn it around. Head back to earth."

McKay let out a very loud sigh. "We've already told you that we can't do that."

"You people are in a lot of trouble. It takes a lot of balls to disobey direct orders and head off to the Pegasus Galaxy when you were told to stay put. Do you really think you can just continue taking what doesn't belong to you and live above the law? You have a day of reckoning coming to you. This could be that day."

Woolsey didn't seem to be phased by Johanson's hostility. "I'm afraid your prophetical day of reckoning will not be happening today. At least not until we undo what has been done. Colonel Sheppard has not yet been informed of the details that we currently know of. Of course, we're still sorting out the details, but we do know a few things. One of those being that we certainly did not go against orders, remove Atlantis from the earth's ocean and set a course back to the Pegasus Galaxy. Had we truly done such a thing, we would have planned a lot better than to leave abruptly without stocking up on necessary supplies and leaving key personnel behind without giving them ample time to settle affairs." He glanced at McKay when he said that.

Sheppard noticed and frowned. _What was that about?_

"We have a situation. Atlantis has been attacked. We did not make preparations to leave earth, Mr. Johanson. Someone else, however, did. Dr. McKay believes that this is happening because of the Ancients."

"The Ancients," Johanson snorted. "I hear a lot of talk about them, but have never seen any proof of their actual existence."

McKay blinked. "No proof of their existence? Look around! Where do you think this city came from? A cracker jack box?"

"This city -"

Woolsey interrupted Johanson. "Let's not lose sight of this meeting. As I was saying, a program of sorts was activated without our knowledge. Several key members were...taken over and the rest of us were affected by some kind of pulse that went throughout the entire city. Everyone - except for those who had been taken over - lost all consciousness and for twenty-four hours, we remained that way. In the meantime, those who were possessed made use of their time by bringing Atlantis into hyperspace on a course back to the Pegasus Galaxy."

This was the first that Sheppard had heard of this. "Really?"

Woolsey confirmed with a nod. "Yes, Colonel. Really."

"So...what you're saying is...we've been hijacked?"

Again Woolsey nodded. "That is correct."

"Ah, well...crap!"

_ _  
>_ 1 _<p>"Effective immediately, all military and non-military personnel will be reassigned as the IOA move in to reassess the usefulness of Atlantis."<p>

The announcement from General Jack O' Neill about floored every one gathered along the stairs of the Control Room five months after Atlantis had set down in the San Fransisco Bay. Most of those present had dreaded that the announcement would come, but even so, they were not prepared for it. Sheppard noticed several IOA members grouped together, wearing their superior looks and smirking as if they had just won a major victory. Particularly Harris Johanson. He turned his head, made eye contact with Sheppard and maintained his smirk, adding a slight nod of victory. Sheppard wanted to deck him one.

Once the announcement was made and every one began to spread out, heading back to carry on with their specific tasks, Sheppard made a beeline for O' Neill with a vengeance. He was firmly convinced that what just happened wasn't right in the least. McKay was right there beside him - obviously feeling the same way judging from the angry look on his face - and as they approached, O' Neill glanced in their direction. He turned and headed for Elizabeth Weir's office...At least it used to be her office a few years ago. In spite of how long she had been gone, Sheppard could hardly bring himself to think of it as Richard Woolsey's office. To be fair, however, the man who was once a member of the NID was now the current head of the Atlantis expedition, and had been for almost two years.

_Was_ being the optimal word.

Not willing to be deterred, Sheppard and McKay both decided to follow O' Neill into Woolsey's office. Unfortunately, there was a slight problem. Johanson seemed to have the same idea. He stepped inside, still smirking, and stood beside O'Neill as if he really belonged there. That was just creepy. Sheppard and McKay stood off to the side as if they were sizing the two up as opponents. Woolsey himself had just taken his seat behind his desk, wearily looking up at them and he wondered to himself if this day couldn't get any worst.

"To what do I owe the pleasure of this visit?" he inquired, feeling defeated.

Before anyone could say anything, Johanson replied first. "You can get out of my chair, for starters."

Woolsey glared up at him.

Sheppard shook his head. "This isn't your office yet, Johanson. By the way, where are your interns? Aren't they always flocking around you like chicks on a farm?"

"If those chicks want to eat," Johanson said, "then they've got to answer to the big bird in the pen. Atlantis will be the best training ground for them."

"They won't know their way around the city!" McKay exclaimed. "None of you will! You...you'll be like a bunch of children playing in a candy shop. You're going to break things, and trust me, you don't want to do that with the city this close to San Francisco!"

"That's why you and several other key people will stay on temporarily to guide us along."

"There's a place I'd like to guide you, alright..."

Sheppard glanced at him. "Rodney..."

"Oh, come on! Please! Like I'm the only one here who wants to tell these morons where they can go? I've had it up to here with all of their arrogance. They have no idea what they're doing! Many of the things they've taken a part are more than likely irreplaceable. They've got no business tampering with technology they know nothing about!"

"That may be," Woolsey said softly, "but the fact remains. As General O' Neill has already announced...the IOA is now in charge of all operations in Atlantis."

"For the most part, all of that is true." O' Neill shrugged his shoulders nonchalantly. "They are going to have complete authority here, including the final decision on what to do about Todd." He glanced at Sheppard as if to say he could have come up with a better name than that for the Wraith prisoner. "But you've still got a few months before you leave Atlantis. As Mr. Johanson has said, many of you will stay on as observers, to lend a hand when needed."

"Observers!" McKay shouted. "Do I look like someone who stands around to observe?"

"No. You don't. But you're going to try it out anyway."

"I don't have to accept this!"

"Yes, you do. It's either that or you can take a walk."

McKay glared at him. Then as if he came to a decision, he abruptly turned and stormed out of the office. Sheppard watched him go, suddenly concerned for the genius. He wondered if there was something else bothering him. McKay seemed to be more cranky than usual.

O'Neill looked at him. Then, he turned to Woolsey and Johanson. "This office is still yours," he said to Woolsey, "and will be until the dust finally settles. That could take some time judging from all the excitement around here. That being the case, I don't believe there will be any reason for a pissing contest from either one of you. Am I making myself clear?" He glared at Johanson as he said that.

Johanson smirked. "I shouldn't have to tell you, General O' Neill, but I don't answer to you."

"No, you don't, Big Bird, but the men who will be stationed here to protect you and your team do and you can sure as hell bet that I can make your life a whole lot more difficult if I so choose."

"Point taken." The look on his face made it clear that he didn't care much for the _Big Bird_ title.

"Good." He turned to Woolsey and nodded. "I'll be in touch." He turned and headed for the door. As he expected, Sheppard followed him. He slowed his pace to let the man walk beside him. "Colonel," he said.

"General," Sheppard returned.

"I seem to recall about six years ago, you were reluctant to join the Atlantis expedition."

Walking down the stairs together, Sheppard shrugged. "I wouldn't say reluctant. Maybe I just wasn't motivated until I sat in the Chair in Antarctica."

"How's your motivation now?"

"Well, sir, I'm not afraid to say that right about now, it just sucks."

O' Neill stopped and turned to face him. "There's always Stargate Command, John. I can get you a posting there. You can still go out and do what you did in the Pegasus Galaxy. Just a little more closer to home."

Sheppard sighed. "With all due respect, sir, Atlantis is my home."

"Atlantis never belonged to us, Colonel."

"Then, why the hell did we go out there and risk our lives in the first place? There are people in the Pegasus Galaxy who need our help. We don't know what the Wraith are doing while we're stuck here battling with BS from the bureaucrats. General...Atlantis is more my home than any other place I've ever visited. But I'm not the only one who feels that way."

O' Neill paused. "It's out of our hands."

"At least tell me what the IOA really plan on doing with Atlantis." He scowled when he saw O' Neill's hesitation. "Come on, General. That bit about reassessing the usefulness of Atlantis is just a load of crap and we both know it."

The General paused. "They want to dismantle it. Break it down. Make it so it can't be used against us. At the same time, all of the major pieces of technology will be sent to Area 51 for further research."

Sheppard swallowed. He felt sick. "You've got to be kidding me."

"Do I look like someone who kids?"

Sheppard didn't answer.

"My offer still stands. Think about it. There's time." With that, O' Neill turned and walked away.

For the first time in his life, Sheppard didn't have any idea what his future held. One thing was for certain. There was nothing bright in it.

Grinning because he was in complete control of the situation at hand, Johanson decided that it was time to put the plan in motion. He stepped out of Woolsey's office, took out his cell phone and made a call. "Cheryl..." he said when the person he was calling answered, "are you ready for that special job I have for you?" He smiled when he heard her eager reply. "Good. Then, let's meet and get it done. It's time to make history."

Teyla Emmagan had just put Torren down for a nap when she heard someone at her door. She expected it to be Sheppard or Ronon, but when she opened the door, she discovered to her surprise that it was three of the IOA interns. The interns, Sheppard had told her, were worst than the IOA members because they would do what they had to in order to get good marks. The more marks, the better the chance to rise up in ranks. Not that the IOA had ranks. They were really nothing more than glorified political diplomats. They had a rule for everything.

Teyla looked at her visitors with curiosity. They were very young, late teens or early twenties. Two of them were women, the other a man. They looked at her with just as much curiosity as she regarded them. One of them, however, had to excuse herself and step away to answer her cell phone. She ended up walking away on some type of urgent request.

"It's okay," the young man said to the other woman. "We don't need her. We'll fill her in later."

The woman nodded. Then, she smiled at Teyla. "Hi. I'm Doreen Stills. This is Jed Meers."

Teyla smiled patiently at them. "Yes. We met a few weeks ago when you arrived with Mr. Johanson and Miss Manor."

"Well," Meers began with a wide grin, "this city is so huge, I barely remember meeting anyone." Then, he pointed excitedly at her. "But how can I forget you and Ronon Dex! I think you guys are awesome...though I probably shouldn't admit that out loud too much. It would be frowned upon by, well, you know. Those in authority above us."

"Yes, well...thank you for the compliment."

Doreen glared at Meers with a look that told him to keep his mouth shut. Evidently, she thought she was running the show. She turned back to the Athosian woman. "Teyla..." She smiled sweetly. "As you know, we really don't know all that much about you or your people. You know...your culture. Your lifestyles. Your transition into an alien city run by people from another galaxy. We would like to get to know you better. You and Ronon Dex. We'd like to broaden our understanding of you and in return, share ourselves as well. After all, we're going to be here for a while. There is so much to learn. Would you be willing to help us out?"

Teyla looked at them suspiciously. "Perhaps another time. I've just put the little one to bed and-"

Doreen blinked. "Little one? Little one what?"

"Torren. My son."

She blinked again. "You have a child?"

Teyla looked at her. "Yes. I do."

Meers shook his head at his intern partner. "How could you not know that, Doreen. That was in the report."

"What report?"

"Oh, it's nothing. The IOA has plenty of files on you and, well, everyone on Atlantis, and we're charged with knowing everything there is to know." He chuckled and waved a fist playfully. "Hence are inquisitive nature. How can we get to know you without asking too many intrusive questions?"

Doreen tried not to sigh too loudly. Somehow she had missed that file. "Don't worry about any report, Teyla. All reports are pretty much just the ones that Mr. Woolsey sends to GC. They eventually come to the IOA...and then, to us."

Meers grinned sheepishly. "The interns. Yeah!"

Teyla really had no idea what to make of him. "I see. Still...perhaps we can meet at another time. How about breakfast on the Terrace? The view is wonderful."

"Well, I think that would be absolutely perfect."

Doreen nodded once. "I agree. Breakfast it is then. Will you be...bringing the little one?"

Teyla decided that keeping her child out of the reach of the IOA was suddenly a top priority. "No," she said, "absolutely not." Then, she went back into her quarters, the door closing behind her.

"I miss you," he said into his phone, leaning against the railing as he stared out at the San Francisco's Golden Gate Bridge.

_"Rodney,"_ Jennifer Keller's voice spoke to him in his ear, _"it's only been three days."_

He frowned. "What? Don't you miss me?"

There was a pause. He imagined she was giving him one of her sly grins. _"Of course, I miss you,"_ she said. _"I just..."_ She stopped.

"What?"

She sighed. _"I wish you were here."_

There was a catch in her voice, and he was surprised that he had actually caught it. Usually, his mind would be so wrapped up in equations or death defying dilemma's that he wouldn't notice. But this time, he did notice. He swallowed. "Jennifer...are you alright?"

_"It's my dad. He's not doing so well and I...They said he isn't going to be with us for much longer, Rodney."_ She took a deep breath. _"I think they're right."_

"Oh, no. Oh, no...Jennifer, I am so sorry. I..." He stopped. He cleared his throat and straightened his posture, even though he knew she couldn't see him. "Okay, look. There's a lot of nonsense stuff going on here at Atlantis, so I'll take a little time for myself...and come out to see you."

_"You don't have to do that. I'm sure you're busy."_

"Hey. You know what? I want to. I really, really want to. Busy or not. Nothing is too important for...for my girl. You know?"

He thought he heard a smile in her voice when she said, _"Thank you. That would be wonderful."_

"Great. Well...can't really come to you in a jumper. Guess the IOA would frown on that, so I'll catch a quick flight and be there in the morning."

_"I'll pick you up."_

"Okay. Great. It's a date..."

_"Good-bye, Rodney. I love you."_

He blinked. His head felt light and his hands were beginning to sweat, but in a good way. He was still not used to these feelings, but he knew he wanted more of it. "Bye, then." He swallowed. "I love you, too." He put his cell phone into his pocket and looked out toward the bridge, deep in thought.

Then, he noticed someone was standing with him. He turned his head.

Ronon nodded once. "Hey."

McKay nodded back, hoping the Setedan hadn't listened to his side of the phone call. "Hey."

They were both quiet for a moment. Then, Ronon said, "Dr. Keller's dad isn't doing so hot?"

"What?" McKay demanded. "Were you listening to my conversation? My private conversation?"

Ronon shrugged. "Well, sure. I don't know what she said...but I heard everything you said."

"What? How long were you standing there listening to me, Ronon? Do you make it a habit to eavesdrop on people's private discussions?"

"Since the first day I became a runner, I learned to listen real well."

"Well, you're not a runner any more, so stop listening!"

Ronon paused. Then, he shrugged again. "Okay. Whatever."

"Fine!" McKay snapped and glared at the Golden Gate Bridge as if it just offended him.

There was a long pause.

Finally, Ronon cleared his throat. "Listen...I haven't got anything to do. If you want someone to go with you to help Dr. Keller...you know, with her dad and everything...I'd like to come along. If you don't mind."

McKay looked at him suspiciously.

"It's not like that. Dr. Keller and I are friends. I'm not going to take her away from you. Besides, she loves you."

"That's right. She does."

"So...Do you want me to come or not?"

McKay nodded. "Yes. Sure. Why not? I'm sure Jennifer would appreciate that you would want to show her support."

Ronon nodded back. "Okay then. I'll go."

"Good."

They fell into silence, keeping to their own thoughts, and looked at the bridge together. Deep down, however, McKay felt grateful that Ronon wanted to help.

Johanson met with his best intern, Cheryl Matire. She was the brightest of them all and that was why he chose her for this mission. She smiled at him eagerly when she saw him, but she wondered why there were two Marines with him.

"What do you want me to do?" she asked him as he came to walk by her side.

He gently grabbed her arm, leading her along. "Come with me. There's someone I want you to meet."

With the Marines following behind, Johanson led his best and brightest intern down a series of corridors. They came to the detention center where a series of cells were. Most all were empty except for the one he led her to. There was a forcefield in place, however, to keep the Wraith that was inside from escape. The Wraith's eyes never left Johanson as they entered. He was fully aware of the two Marines and the young woman, but his interest peaked at Johanson.

Cheryl stopped with the Marines right behind her, startled at the sight of the Wraith.

Johanson didn't mind. He moved ahead of her and came to a stop directly in front of the cell's forcefield. He smiled grimly at the Wraith inside. "Todd, I presume."

The Wraith called Todd nodded once imperceptibly. He took a brief moment to try to see into his visitor's mind. He saw many things...and it made him smile. "Greetings to you...Remington Harris Johanson."

Johanson smirked. "I do believe that you and I are going to become...friends."

"Indeed." Then, Todd laughed.

_ _  
>_ 2 _<p>Zelenka didn't care much for the IOA presence around him. In his native Czech language, he occasionally rattled off a string of curses because of the woman at his side who represented the accursed coalition. Whether he considered it as fortunate or not, Patricia Manor had no idea that his disgruntled demeanor was aimed directly at her. He and his team - curse McKay for leaving - were in the midst of turning over everything they had to the new caretakers of Atlantis and they were not happy about it at all.<p>

Zelenka kept his eyes focused on the monitor of his laptop on his work station as he worked, aware of the annoying woman peering over his shoulder. The others around them at their own stations in the Control Room had their IOA shadows as well. He cursed some more.

"You seem to be very passionate about your work," Patricia told him, smiling encouragingly at him. "That's always so refreshing to see."

He took the pencil out of his mouth and turned to regard her as if she were a bug under a microscope. A dead squashed bug, for that matter. "What?" he said impatiently.

"I said you're very passionate about your work. That's a very attractive quality in a man." She smiled at him.

He glared at her, wishing she would just shut up and let him work. He sighed and looked at the notes in his notebook. Then, he blinked. _Did she just say that she finds me attractive?_ He turned his head slightly to look at her again. She really was a pretty woman, but unfortunately she was also IOA. Anything IOA was simply not attractive. He cleared his throat. "Yes, well...I do happen to love my work. The last five years of my life have been amazing." He looked around, sadly shaking his head. "Unfortunately, that's all about to end."

Patricia leaned toward him. "Maybe it doesn't have to end."

"What do you mean?"

"You could stay on. We're still going to need many of your staff to help us even after the transition."

"That may be...but I'm afraid one of them won't be me. After this, I'm done. If we can't be out in the Pegasus Galaxy, keeping our planet and those we left behind safe from the Wraith, then there's nothing left for me here." He made eye contact with her. "You'll find that that's the consensus around here."

Patricia frowned. "Oh. Well...I'm very sorry to hear that."

He nodded. Then, he went back to work. That was until a shout came from his left from Chuck Campbell, one of the technicians. "Dr. Zelenka! I think you should see this."

Sighing impatiently, he moved away from his station and moved toward one of the main monitors on the wall. Campbell was at the work station, frowning at the monitor with what looked like growing concern. Major Lorne, who had been standing off across the room, joined them when he saw the commotion. The monitor showed an interior schematic of the city. A red flashing dot had recently begun to show when it wasn't there seconds before.

Campbell tapped at it with a worried frown. "I don't think that's supposed to be doing that."

"It's nothing," Zelenka said with a shrug. "Probably just a glitch in the system." In spite of what he said, he moved in for a closer look, aware of Patricia standing closely beside him.

Lorne nodded his head toward the blinking dot on the screen. "Why is it doing that?"

"Like I said...probably a glitch." Suddenly he tensed and cursed in Czech.

"Something tells me that's not really a glitch."

Zelenka abruptly turned and made a bee-line for Woolsey's office. Stunned, Lorne and Patricia trailed behind. They followed him directly into the office where Woolsey looked up from his desk.

"Doesn't anybody believe in knocking any more?" he asked, knowing he wouldn't get an answer.

Zelenka got right to the point. "We need to get Atlantis out into space. Now!"

Woolsey frowned. "Dr. Zelenka, believe me. I share your concerns, but you know as well as I do, that isn't possible."

"With all due respect, there will be no San Francisco if we do not get Atlantis out of here now."

Lorne and Woolsey suddenly looked concerned. Patricia just looked confused.

"What are you saying?" Woolsey demanded.

"Something in Janus' secret lab is causing an unusual amount of energy back into the ZPM. It's overloading the unit! If we don't stop it, it will be just as if we've been hit by several nuclear bombs."

Sheppard was trying to make his foul mood go away by running along the terraces of the city. The view was always spectacular, but right now, that was the only good thing about being back on earth. The view. After all, he didn't have anything on earth that was his. He was from earth. He was born and raised on the big blue ball. But there was nothing to keep him there. In his heart, he already missed the Pegasus Galaxy, and that even surprised him. He hadn't realized he would miss being out there against an alien race bent on keeping humans as livestock. That was what bothered him the most...He had been making an actual difference. Not just for earth, but for other people who lived on other far distant planets.

Now he wasn't doing a damned thing but getting mad.

So he ran.

McKay had stormed off the other day and no one knew if he was even going to be back. Sheppard felt that he was actually proud of the guy for standing up against the IOA. He found himself wondering why he wasn't responding in the same manner. Johanson hadn't been happy about it and made a personal vow to keep McKay off Atlantis forever. A mistake, of course, because McKay's genius got their butts out of the fire more than once. Not that he would admit that out loud.

He came around a corner and had to come to a stop because someone was standing directly in his path with her arms folded across herself. Coming to a stop, Sheppard could see that he could be in for a bit of trouble.

"Teyla," he said with a nod.

"John." Teyla uncrossed her arms, dropping her hands to her sides. "You have been avoiding me."

Sheppard let out a sigh and moved to lean against the railing. "That's not entirely true." He paused. "I've been avoiding everybody."

She moved to stand next to him. "What is troubling you?"

"Aside from the fact that we're stuck here on earth, not going back to make a difference, and all of us are going our separate ways?" He shrugged. "Not a damned thing."

"I'm sorry. I realize how hard this is on you."

"On me? What about you, Teyla? You must feel pretty bad being stuck here with Kanaan worrying about what's happened to you and Torren."

She paused in thought. "I have to believe that we will be going back. Otherwise, it will have all been in vain. Or perhaps it will only seem that way, but sometimes the absence of a purpose can make us forget how much good we have done."

Sheppard looked at her. "Well, one way or another, I'll get you back home. I promise."

"John, you do not have to promise me anything."

"If you and Ronon get stranded here because of bureaucratic bullcrap from the IOA, I'm not going to let that stand. And I can think of quite a few people who feel the same way." He was about to say more but was surprised to see Woolsey, Johanson and Patricia heading right for them. "Something's going on."

"What?" Teyla asked, curious. She turned her head to follow his gaze.

That's when the others reached them.

"Colonel," Woolsey said without hesitation, "we have a serious problem. Dr. Zelenka discovered a massive powersurge flowing directly into the ZPM. He says if he can't stop it, it will cause an explosion that will rival Hiroshima."

"What?" Sheppard exclaimed. "When did this happen? Can he stop it?"

"At the moment, he can't. The power surge is coming from somewhere in Janus' secret lab."

"Well, can't he find out what's causing it and shut it down?"

"That's the problem. The room is sealed shut and we can't get inside. From what Dr. Zelenka can tell, when the power surge began, the room went into a lockdown mode. It sealed itself. So the problem is, if we can't get in there and shut it down within twelve hours, we're all going to die." He looked grim. "And we'll take San Francisco with us."

Johanson glared. "Unless this is a trick and you're trying to find an excuse to go back to the Pegasus Galaxy."

Sheppard wanted to ignore him, but what he had said bothered him. "What the hell are you talking about?"

"You're scientist suggested taking Atlantis back out into space. So who's to say that isn't the plan all along?" Johanson took a menacing step forward. "You bring the city out to space, stop the so called bomb threat, and then open up a hyperspace window to return back to Pegasus."

"You know what? You're out of line and you're really starting to piss me off." Before the man could respond, Sheppard turned to Woolsey. "Okay, so here's what we do. We take a jumper and go get McKay, then -"

"That man is not to step foot anywhere in this city," Johanson interrupted. "He made that decision when he left."

Teyla shook her head. "He left for a family emergency. Not because -"

Sheppard raised a hand. "Teyla, it doesn't matter, because I'm still in charge of the military presence here and I say we get McKay,and bring him back to fix this. I'll take a jumper out and be back before you know it."

Woolsey shook his head. "Colonel, I think you should stay."

"Why?"

"Because we may need you in the Chair if we have to leave in a hurry. We can get Dr. Beckett to fly the jumper." He paused. "No offense to Dr. Beckett, but I think your presence here at this time is more required than his."

Sheppard nodded. "Okay. That makes sense. I'll have Major Lorne go with him."

"I can go, too," Teyla replied.

"Great. Then, let's get it done." He headed back into the city with the others following behind.

McKay and Ronon had gone to Chippewa Falls, Wisconsin, by flight, but they had been joined by one other person. Ronon had decided to invite Amelia Banks. McKay hadn't known what to think about it. It had thrown him off guard, but on the other hand, if Ronon was busy looking at Amelia, then he really wouldn't try to take Jennifer away from him. Jennifer had picked them up from the airport. She was surprised to see Ronon and Amelia but appreciated their support. She sat in the back seat while Ronon and Amelia sat in the front. Ronon drove, assuring everyone that he had driven quite a bit the last time he visited earth with Sheppard.

At the Keller household, Jennifer's relatives came and went, dropping by to offer any help or comfort, bringing lots of food. The family were also appreciative of the support from Jennifer's colleagues, though many of them could not take their eyes off from Ronon. They had never seen anyone like him.

Jennifer had introduced briefly her friends to her father, whom expressed his gratefulness to them for their kindness to his only daughter. He reached out and grabbed a hold of McKay's hand, squeezing it affectionately. "Now...you, young man, must be...must be the one responsible for...the happiness in my...little girl's eyes." He nodded, making eye contact with him. "Even though she's sad for...my current state of affairs...I know she's at least thinking...of you...You have my blessing..." He nodded once, smiled and sat back into his pillows with a contented sigh.

"Really? I do?" McKay inquired, not knowing what to do or say. He looked at Jennifer for help.

She smiled and gently took his arm. "Come on, Rodney. I'll take you to get something to eat."

"Okay, but...but I want to know what you mean by blessing," McKay said, turning back to Jennifer's father. To his amazement, he found that the man had fallen asleep. "Oh."

Jennifer took him into the kitchen. She packed some food into a basket, took McKay by the hand and led him outside into the backyard. Hand in hand, they seemed to be heading for a path, which went into the woods.

"Where are we going?" he asked her.

She smiled at him. "You'll see."

They continued down the path in silence, which was hard for McKay. Usually he rattled off about bugs and allergies, but with Jennifer, he was actually quite content. Judging from the look on her face, she seemed to be as well. She led him further along the path and suddenly off from it. They went through some wooded area and abruptly, the sky was ahead of them. McKay put his hand up before his eyes to shade them from the sun, and when he did, he realized they were standing on a cliff overlooking miles of rolling hills with mountains in the background. The sight was breath taking.

"Wow," McKay said, "that's...that's pretty amazing."

Jennifer sat down on the rocks and set the basket down beside her. "My father used to take me here when I was a little girl." She paused. "I felt so small. Here I was, just a little girl in a very big place."

McKay took his time sitting next to her. He wanted to make sure there were no bugs nearby.

"I always felt so tiny in this place. Like I was just a little speck who couldn't possibly make any kind of a difference in a place where it's so easy to be overlooked." She paused to take in the view. "My father told me that in this place, it was just the opposite. It wasn't me that was overlooked, but this huge place I was standing in. He told me that it was easy for him to ignore where we were as long as I was with him. In watching me here, he saw that where we were made a difference and because of it...it would enable me to make a difference, too."

McKay smiled at her. "You make a difference, Jennifer, every where you go. I shouldn't have to tell you that you've made a difference in me."

She watched him. "Oh, really? In what way have I made a difference in the life of Dr. Merideth Rodney McKay?"

"Well...I think I'm just a little bit nicer than I used to be." He showed her a tiny space between his thumb and forefinger. "Perhaps not a lot, but just enough where I come out of the shell I've been living in."

"You have a shell?"

"Oh, come on. All arrogant great scientific minds have some kind of a shell." He paused. "I'm...I'm really just surprised that of all people, you were the one who managed to get inside." He shrugged. "I know I'm not the easiest person around to get to know. I mean, let's face it. If I weren't me and met me, I don't think I could be friends with me, much less strike up a conversation. Of course, if there were two of me and we got into a conversation - almost like the time when we met replicators like us - I'll bet we could talk for hours. Maybe even days."

She laughed and shook her head. "You are something else, I'll tell you that." She hugged him. "Thank you for coming."

They sat in silence for a while, enjoying the view and each others company. Jennifer opened the basket and shared the food. As they partook of it, McKay glanced at her. "Jennifer," he began, "do you...do you have any idea what you would like to do now that Atlantis is going to be used by the IOA?"

She thought about it for a moment. "Well...I guess there really is no going back, is there?"

He frowned. "No."

"To be honest, I don't want to think about it. Right now, I'm here for my father. I'm not going any where."

"Really? Oh, well...then...then, I won't think about it either. How's that? You'll be here for your father, and I'll be here...for you."

She smiled at him. "That would be nice."

It almost was nice, until McKay almost choked on a mouthful of food when a jumper decloaked right in front of the cliff they were enjoying a picnic on.

_ _  
>_ 3 _<p>Dr. Carson Beckett had managed to find a small clearing where he could land the jumper. He, Lorne and Teyla waited a short time for Jennifer and McKay to join them. Once they were inside, Beckett cloaked the jumper just in case someone from the Keller residence came looking for Jennifer. Lorne reclosed the hatch.<p>

"Rodney," Beckett began to say in his thick accent, "we don't have much time. We have to get you back to Atlantis as soon as possible."

McKay snorted. "I'm not going back. I'm sorry to have wasted your time, Carson, but you made this little trip of yours for nothing. Besides, there isn't any type of catastrophe that could make me come back. I am completely done with Atlantis."

"I wouldn't be so sure. You don't know what's happened."

"The only thing that's happening there is that it's being overrun by pompous bureaucrats who have absolutely no idea what they're doing. If I were you, I'd leave. Go back home to your mom, for all I care."

Beckett sighed. "My mom thinks I'm dead and you should bloody well know that." Then, he shook his head. "But that isn't the point right now."

"Then, do tell!"

"Atlantis is about to blow up," Teyla told him. "Is that the short version you needed to hear?"

Jennifer frowned. "Blow up? What do you mean?"

"The ZPM is reacting to some kind of power surge," Lorne tried to explain. "In short, from my understanding, it's being overloaded. If the overload continues, it will detonate the city and the resulting explosion will take not only Atlantis but San Francisco as well."

McKay almost laughed. He smiled at them and waved a confident hand in the air. "No, no, no. What you've just described is impossible. There is no possible way to overload a ZPM. There's too many safeguards built in by the Ancients. You'd be hard pressed to rig a ZPM to blow up. I could do it, of course. It's child's play really, but it's just not going to happen. So go on back to Atlantis and tell everybody that it's all a big mistake."

Lorne shook his head in disbelief. He thought he remembered that the Goa'uld had tried to rig a ZPM to explode back on earth when O' Neill took command of Stargate Command as General, but he decided not to mention that. "Are you kidding me? Do you think we'd come all the way down here to tell you that a mistake is going to destroy Atlantis and everything around it?" He leaned forward. "We've got less than twelve hours!"

"Eight hours now," Beckett said with a sigh. "It took us over four hours to get here."

"Rodney," Teyla said, stepping closer to him. She placed a hand on his arm and looked into his eyes. "We're not making this up. Something in Janus' lab has triggered this, so whatever can be done to stop it must be in there. You're the only one who stands a greater chance at stopping it. Dr. Zelenka can't even get back into the lab. He needs your help."

"He can't get into the lab?" McKay scowled. "Well, why not?"

"Because when the bloody overload began," Beckett snapped, "the lab sealed itself shut. Are you coming or not?"

Jennifer looked at him. She rubbed his back affectionately. "I think you'd better go. If anyone can stop it, it's you."

McKay frowned. "But what about you?"

"I'll be fine. I know you want to be with me, Rodney, but lives are at stake and you really are the best chance at stopping it. So go stop it and come back to me. Okay?"

He paused. "Okay...I'll go."

"Is Ronon here with you?" Teyla asked Jennifer.

Jennifer nodded. "Yes. I'll tell him to come if you can wait a moment."

Beckett sighed. "I don't mean to be indifferent to your own personal grief, Dr. Keller, but we need to go so as soon as you get him, the better."

"Okay." She kissed McKay and then hurried off to find Ronon.

McKay watched her go. When he couldn't see her any more along the trail, he turned back into the jumper only to find Beckett, Lorne and Teyla watching him.

"What?" he demanded. "It's not like I haven't been kissed before." He turned to Beckett indignantly. "And by the way, she's a better kisser than you could ever be."

Beckett rolled his eyes. "It figures you would still remember that so easily."

Teyla and Lorne exchanged looks. Lorne could only shake his head. "Why is it whenever there's major trouble, we always seem to have to rely on Dr. McKay to get us out of it?"

"You have some explaining to do," Patricia said, glaring at Sheppard. She had intercepted him in the corridor out side of the mess hall as he was on his way to check on Zelenka's progress.

Sheppard came to a stop, slowly turned around and looked at the IOA woman. He idly wondered where Johanson was, but then realized he really didn't care. "Explaining to do about what?" he inquired as calmly as he could. He really didn't like the IOA. They gave him a headache.

"We've seen your files. We know of your accomplishments. I'm sure that while others would applaud your bravery and heroism in the face of insurmountable odds, there are others still who see you from what you really are. A glory hound. All guts and glory." She took a menacing step closer to him. "You don't even care about who you hurt or who you get killed in your quest for fame and fortune, do you, Colonel Sheppard?"

"I wasn't sure before, but now I am." Sheppard glared back at her. "You really don't have any idea what you're talking about."

"I know exactly what I'm talking about. I'm here to see you pay for what you did. There isn't a place in this city where you can hide from me or the truth. I'll have it all. And then I'll have your head on a silver platter."

He stepped back and frowned. This woman had an axe to grind with him and he had no idea why. "What am I supposed to be paying for exactly?"

"Colonel Marshall Sumner." She glared defiantly at him. "Does that name ring a bell?"

Sheppard froze. He swallowed hard at the memory. When they first discovered the Wraith, one of the first casualties of war had been Colonel Marshall Sumner and by his own hand. "Yes, I remember him."

"You killed him."

"I did."

"For glory and fame. So you could be the head of the military presence on Atlantis. You won't get away with that. I'll see to it personally."

He sighed. "You've got it all wrong. I don't do any of this for fame and glory. I shot Colonel Sumner because the Wraith were torturing him! Draining years of his life by inches!" He shook his head. "I saw the look in his eyes. He didn't want to go out that way."

"So you made the decision yourself. And you shot him. You killed him."

He nodded. "I shot him. I ended his torment. I let him die with dignity and honor. Believe me, there's nothing dignified or honorable about dying by the Wraiths hands." He scowled. "You sound like this is personal. Who was Colonel Sumner to you anyway?"

"Colonel Sumner," Patricia said through clenched teeth, "was my uncle."

Before Sheppard could think of a response, she turned and walked away. With no other choice before him, he turned and continued to Janus' secret lab where he found Zelenka.

"You've been at it for eight hours, Radek!" Sheppard exclaimed. "Didn't opening the door the first time have to do with some kind of music?"

Zelenka glanced at the hallway, which ended with a wall that should have been a doorway. Or at least a doorway in the wall from which a person could pass through. But for some reason, the wall felt as solid as it looked. McKay and Dr. Daniel Jackson had worked together at finding a way - using three light fixtures - to sound out some kind of code. The chimes had sounded, and if correct, they would have made it possible for anyone to walk through the wall, thereby entering the secret lab of Janus.

In theory, it still should have worked that way.

"Unfortunately, Colonel," Zelenka said with a shake of his head, "the same variation Dr. McKay and Dr. Jackson used is no longer working. In fact, none of the six variations are working, so this puzzle is no longer a simple solution." He glared at the laptop he held in his hands as if it had a secret and wouldn't tell him. "We've tried everything!"

"We could blast that wall to hell!"

"No, we couldn't. We've already gone over that. This isn't just about getting through the wall. There's some kind of forcefield around the interior of the lab. This means, we could blow a hole in the wall, but the forcefield would only still be there. I think we should use the Chair and get away from earth as fast as we can. The Daedalus should be able to beam us out of here if we don't have time to stop it."

"Well, most of Atlantis has been evacuated, with the exception of those who really need to be here." Sheppard let out a deep sigh. "Don't worry about that. I managed to get rid of most of the IOA, too, but we still have Atilla the Hun and his minions."

Zelenka glanced up at him. "We may have another problem."

"What?"

Zelenka paused. "The power surge might get worst if we try to activate the Chair. We could blow up the city by attempting to leave."

Sheppard scowled. "You've gotta be kidding me, Radek! Don't even joke about that."

"Do I look like I'm joking?"

"Where the hell is McKay!"

"Look, I've been trying to get us in there. If he can do any better, then now would be the time!"

As if on queue, McKay's voice came over the intercom. _"Sheppard! What the hell did you guys do?"_

Sheppard frowned, tapping his ear piece. "What do you mean, what did we do? We didn't do anything! Janus did...or something in his lab did."

_"Carson tells me the lab is sealed."_

"Carson is right. It is. We can't get in. Zelenka tells me that blowing the wall up won't even get us in there because of the forcefield."

_"Forcefield? There's a forcefield in the lab? When did that happen?"_

"How the hell should I know. When are you getting here?"

_"Carson's parking the jumper now. I'll be there in a few minutes."_

"That's just great." He looked at Zelenka. "You might as well get back to the Control Room. McKay might need you there to monitor our situation."

Zelenka nodded, muttered in Czech and stormed off. Sheppard put his hands on his hips, glared at the wall and said, "Crap."

"It's the only plan we have, General," Woolsey said grimly. "With Colonel Caldwell ready to beam us onto the Daedalus, at least we'd have that to fall back onto if this should fail."

General O' Neill smiled reassuringly at him from the viewing screen in the Control Room. _"That's not going to happen, Richard. The Daedalus has other matters to attend to. I have another avenue of assistance I can give you. She'll be contacting you soon."_

Woolsey frowned, puzzled. "She?"

"General," Johanson began, taking a step closer to the screen, passing Woolsey, "I want you to know that I intend to lodge a formal complaint about Richard Woolsey's command, and his entire expedition team. That includes all of the military presence on Atlantis."

O' Neill looked at him. _"Johanson, shut up."_

Johanson stared. "Excuse me."

_"Let me put another way...if you don't shut up, I'll order the military presence - every single one of them - to throw your ass over the highest terrace." He focused his attention to Woolsey. "Richard, you do what you see is absolutely necessary to get Atlantis safe. If you have to take her back to the Pegasus Galaxy to stop this thing from happening, go for it. But expect help soon. You're not alone in this."_

After the connection was gone, Woolsey approached Johanson, Patricia, and their aides. "Whatever you may believe, I assure you, the danger is real. You may want to remove yourself from Atlantis to save yourselves."

Johanson glared at him. "We're not going anywhere."

"Suit yourself."

At that point, Zelenka appeared, cursing up a storm in Czech. He took his station and noticed that Patricia came over to stand beside him. He tried not to think about it as he set his laptop on his work station. By this time, McKay should be at the secret lab.

They were all there. Sheppard, Teyla, Ronon, and McKay. McKay looked at his monitor as he stood in front of the wall, frowning. He looked at Sheppard, frowned again and shook his head, muttering to himself.

"Can you get us in there or not?" Sheppard asked impatiently.

Mckay frowned. He sighed and pointed at the light fixtures. "Hit the fixtures."

Sheppard shook his head, but he did as McKay asked. He tapped them so that three chimes sounded.

"Okay...now do that again, but the other way."

"Rodney...Zelenka already did this."

McKay rolled his eyes. "I'm sure he did, but even six simple variations have to be in a certain sequence. Just humor me."

Sheppard exchanged looks with Ronon and Teyla. Then, he tapped the fixtures again, going the other way.

McKay nodded with satisfaction. "Okay. Good. That's very good. Now...tap it again the original way."

Sheppard wanted to hit him. "What original way are you talking about?"

"The original code. The first one you just did."

"And why am I doing that?"

"We just reset the code so that it will work again. Will you please just trust me and do it?"

Ronon couldn't help but grin as he looked at Sheppard.

Sheppard took a deep breath. He hit the fixtures again.

"Okay...now follow me." McKay walked right into the wall...and through it.

Sheppard blinked. Maybe it was that simple. "Okay...let's do this." He followed.

Ronon and Teyla followed behind.

A few seconds later, the four of them were standing in the lab. McKay was at a control panel, but something was wrong. "No, no, no, no. Oh, no."

Sheppard didn't like the sound of that. "Rodney..."

"I was afraid of this. When you said Zelenka detected a forcefield, I thought it was to keep us out, but we went through it like butter."

"So if it doesn't keep anyone out..."

As a test, Ronon turned as if he was going to head back out. Immediately, he met heavy resistance and was thrown backward to the floor. "Damn," he said as Teyla helped him up.

"It's meant to keep us in the lab," Teyla replied grimly.

Sheppard glared at McKay. "Can you shut off the forcefield and stop whatever the hell is going on with the ZPM?"

McKay looked at his laptop and then at the monitor on the workstation he was at. "Yes...I can. But it's going to take some time." He put the laptop down and began to work on Janus' control panel.

"You better know what you're doing, Rodney," Sheppard said.

McKay rolled his eyes. "Oh, come on! How many times have I pulled our bacons out of the fire? Trust me, okay? I know what I'm doing." He suddenly looked happy. "This might even be over quicker than I thought. All I have to do is reroute the power surge...and slow it down...Oh, and right here, I can turn off the force field with a simple click of a button." He pressed it.

An indicator on the monitor screen went from green to red.

"Oh, no." He got up and backed away from the station.

Ronon, Teyla and Sheppard couldn't help but be bothered by what just happened.

"Rodney, what the hell did you just do?" Sheppard asked.

Before McKay could respond, all four of them vanished in a bright white flash of light.

_ _  
>_ 4 _<p>At the Control Room, Zelenka was working at his work station...or more to the point, he was waiting for McKay to tell him what to do. McKay always told him what to do. When he didn't get any instructions, he began to worry, only because it was completely uncharacteristic of McKay not to be telling him or anyone else for that matter what to do.<p>

That's when Campbell, who was checking over the life signs detector on the main monitor, noticed something unusual. "Uhm...Dr. Zelenka...they're not here."

Zelenka tried to ignore the alluring presence of Patricia Manor as he glanced toward Campbell. "They're not here? Who's not here? And what are you doing?"

"I was monitoring life signs to see how many people we still have in the city, and if we need to get more of them evacuated...but that's when I saw this." He pointed at the screen.

Zelenka moved his chair closer. "Is that the lab?"

"Yes, it is." He turned to look at Zelenka. "A few seconds ago, there were four life signs in there. Now, there aren't any."

"Then...they left the lab."

"They didn't walk out of the lab, doctor. If they had, we'd be able to trace them. They just blinked out...as if they vanished."

Zelenka slapped his ear piece. "Dr. McKay." There was no response. "Dr. McKay...Colonel Sheppard? Teyla?" No one answered his call. He abruptly got out of his chair and headed for Woolsey's office. He was dismayed to find that Johanson was there as well, but that really couldn't be helped. "Mr. Woolsey, we might have a problem."

Woolsey looked up at him. "You mean...another problem? Or a slight variation to the problem we already have?"

Zelenka hesitated. "I'm not sure...but Colonel Sheppard, Dr. McKay, Teyla and Ronon are not in the lab. And according to our life sign detectors, there not anywhere in the city."

"What?"

"They're just gone!"

Woolsey rose to his feet. He tapped his ear piece. "Major Lorne, I need you to take a team to the lab and start a search for Colonel Sheppard and his team. Leave some men at the lab. I'll be sending Zelenka there to see if he can't try to figure out what is happening."

_"Understood,"_ came Lorne's response.

Zelenka headed for the door.

"Hold on," Johanson growled.

Zelenka stopped. "What is it? We're rather busy around here."

"I'm coming with you. This charade has gone on long enough."

"You call it what you want. This charade is going to kill us if we don't stop it!"

Zelenka left the office, and Johanson followed.

When they were gone, Woolsey tapped on the ear piece. "Major Lorne..."

_"Go ahead,"_ came Lorne's voice.

"I've got an idea."

Major Lorne sent his men out to protect Zelenka in the lab and to search the city for Sheppard and his team. After all, if there had been a threat to the team, they had to be prepared for that same threat to be real for Zelenka. Lorne headed for what they called the Zero Point Module room. Without wasting any time, he headed right for the triangular table which housed three ZPM's, of which only one of them was currently working. In fact, it was being filled with power from something no one understood from Janus' secret lab.

He tapped his piece. "Mr. Woolsey, I'm looking at the ZPM now. You do realize that if I take it out, we'll lose the cloak and we'll be seen."

Woolsey's voice came back. _"I'm well aware of what might happen. I just don't want there to be a massive explosion. So in light of the risks, Major Lorne, I think allowing ourselves to be seen in the Bay outweighs the deaths of millions of people. Don't you?"_

"I do."

_"Then take out the ZPM."_

Lorne took a deep breath and began to activate the panel to release the ZPM.

Zelenka and Johanson arrived at the lab to find two marines standing at attention in front of the wall. Johanson glared at them and then looked around. "Where the hell is this lab you've been talking about?" he demanded to know.

Zelenka pointed at the Marines. "It's behind them."

"Nice try. There's nothing but a wall behind them."

Zelenka snorted, walked in between the guards...and through the wall. Johanson stared after Zelenka in astonishment. Up to this point, he had actually believed that everything which had been happening was a scheme to get Atlantis back to the Pegasus Galaxy. He still believed that. But perhaps there was something else going on.

He took a deep breath and headed for the wall...and he walked right through it. Amazed, he stopped and simply stood there to take a look around. "Well, I'll be a son-of-a-bitch," he said softly.

"I wouldn't blame your mother for your disposition if I were you," Zelenka told him as he began to look at the monitor at a station where McKay had left his laptop. He thought he saw the source of the power surge but then realized that the actual source was hidden. However, it was somewhere in this lab and he intended to find it. As to what happened to McKay and the others, he could only hope it wouldn't happen again.

He sat down at the console and began to carefully trace the power surge. He found a program that was protecting the source, and also noticed something else. He tapped his ear piece. "Mr. Woolsey, I'm in the lab and I have discovered that the force field I detected earlier is gone. I believe it deactivated itself once whatever happened in here with Colonel Sheppard and his team happened."

There was a pause. _"What about the power surge?"_

"I'm tracing the source. I believe it is coming from a device somewhere in this lab. If you give me a few moments, I should be able to locate it and see about shutting it off."

_"That's good news, Dr. Zelenka. I'll have Major Lorne hold off on taking out the ZPM."_

Zelenka blinked. "You ordered Major Lorne to pull out the ZPM? You have to stop him! With this type of surge, pulling out the ZPM could have a negative effect! Like a spark, it could blow up prematurely!"

_"Alright, I'll tell him to stop...if it's not too late."_

Zelenka turned to glare at Johanson as if it were his fault. He cursed in Czech. Then, he said, "That's the problem with people today. There are no discussions. Simply orders and plenty of mistakes. Where's the communication?"

Johanson just looked at him.

_"Major Lorne,"_ Woolsey said urgently into his ear piece, _"I implore you to stop what you're doing immediately. Do not take out the ZPM!"_

In the ZPM room, Lorne was just about to take it out. He had his hands on it, but he stopped. "Is there a problem?"

_"It seems that there is,"_ Woolsey replied in his ear. _"It seems that if you pull it out now, it might explode earlier than if it were to remain in the module housing unit. So whatever you do...do not remove it."_

Lorne took his hands off from the ZPM and pressed a button. He watched the ZPM disappear back into the generator. "Good timing, Mr. Woolsey."

"Tell me about it."

Zelenka was just about to find the source. His eyes grew wide as if he was about to discover a great treasure. Johanson paced around the room with his arms folded across his chest. He tried to look at everything. There was so much to take in.

"Did you find what you're looking for yet?" he asked.

Zelenka waved at him impatiently. "No. Now be quiet. I'm on to something here."

Johanson glared at him. Suddenly, there was a bright flash of white light. He blinked and put his hands over his eyes. "What the hell was that?" he demanded. He blinked again and found that his eyes were trying to adjust. Someone was standing in front of him. At first he thought it was Zelenka, but then he thought it was Ronon.

It was Ronon. Without a word, Ronon leveled his gun at him and stunned him. As Johanson fell to the floor, Ronon turned to Zelenka and fired a shot at him, too. Teyla and Sheppard pulled the unconscious man off from the chair and dropped him onto the floor. McKay sat down without a word and began to type on his laptop. Then, he turned to the control panel and commenced work there.

Sheppard and Ronon exchanged looks with each other. Then, they walked out of the lab. Once they saw the Marines, Ronon shot them both. He and Sheppard dragged their unconscious bodies back into the lab.

_"Mr. Woolsey, this is Colonel Samantha Carter of the George Hammond standing by to assist you,"_ replied a smiling Carter from the monitor screen in the Control Room. _"I have a present and would like to beam it down to you if you don't mind."_

Woolsey looked startled. "Why, thank you, Colonel. I can't imagine why you would be sending a gift. I'm just glad you're available to help us out." He hesitated. "In fact, we do have a snag. It seems we've lost Colonel Sheppard and his team. They don't seem to be anywhere in the city."

Carter looked concerned. _"That's odd. I'm sorry to hear that. What can we do from up here?"_

"Just continue to stand by. I see no reason for you to send anyone down here to assist us. Any time we're dealing with something that belonged to Janus, you never know what's going to happen. Everything is just completely unpredictable at this point."

_"Well, let me beam down that gift."_

"Can't that wait?"

_"I'm afraid not. General O' Neill was very adamant about getting it to you at all costs. He said it was a top priority."_ She nodded to someone off screen. Then, she smiled at Woolsey from the screen. _"It should be perched right onto your desk. We've refined beaming technology to near pin-point accuracy. If that item isn't on your desk, I'll retire to a desk job."_

"Thank you again, Colonel. I appreciate your help."

_"You're welcome."_

The transmission ended and the screen went back to displaying the schematics of the city. The life signs detectors were still showing, and he immediately noticed that there were six life signs in Janus' lab.

"Major Lorne," he began...but he didn't get to finish what he had been about to say. A bright white light appeared around them all and then vanished. When it did, they all dropped to the floor in unconsciousness. In fact, it worked that way throughout the entire city. Everyone who wasn't in the secret lab lost consciousness. Even Todd in his cell dropped to the floor.

When the pulse ended, Sheppard, Ronon and Teyla left the secret room. McKay remained behind to continue his task. Ronon and Teyla wordlessly went up to the Control Room. Sheppard headed for the Control Chair. McKay's fingers worked furiously over the console panel. The surge was stopped, but it had also done it's duty. The ZPM was fully charged. It wasn't a power surge but a power supply.

Sheppard sat in the Chair. It came to life and reclined. He thought of the destination they needed to get to and brought the city to life. Outside, the city rose out of the water and took to the skies. Once it rose high enough, the cloak was gone and the shields were at full power.

In her command chair on the George Hammond, Colonel Carter stared in astonishment as the city began to break free from the earths entry. "Why didn't they tell us they were breaking free?" she asked no one in particular. She glanced to one of her men. "Hail them."

"I'm trying," the man said, "but they're not responding."

"Keep trying." She rose out of her seat and stepped closer to the screen. She watched as the city came out and broke free from earths orbit. Suddenly, a hyperspace window opened and Atlantis went into it. Then the window closed, and the city was gone.

_ _  
>_ Epilogue _<p>"Ah, well, crap," Sheppard replied, after hearing about the hijack. "If there's one thing I can't stand, it's possession. So who possessed us and why?"<p>

McKay shook his head. "We weren't exactly possessed. More like...our brains received a download that temporarily gave us a new program to follow. Once it was carried out and the program had run its course, it became obsolete and deleted itself."

"Are you saying some kind of computer program was installed into my brain and caused me to be a part of this hijacking?"

"Yes." He scowled at the look of disbelief on Sheppard's face. "Oh, come on. It's not far fetched, you know. Our brains are like computers, and Janus obviously didn't have any problem learning how to do it. Besides, something similar did happen to me, if you recall. And it's also not unlike what happened to General O' Neill."

"So Janus is responsible?" Ronon asked. "This thing that happened is because of him?"

"It would seem so. It happened in his lab."

"The question we should be asking," Woolsey began, "is why now? Why did this happen now?" He paused as he leaned forward. "Just before the four of you took over Atlantis and set us on a course back to the Pegasus Galaxy -" Johanson let out a snort of disbelief to which Woolsey pointedly ignored. "- you were in the lab. Suddenly, you disappeared. As far as we know, you were no longer any where to be found on Atlantis. Do you have any idea where you were? Obviously, wherever that beam took you, it's where this download happened."

Ronon shrugged. "I don't remember anything, really. I thought we were in the lab."

Teyla pursed her lips in thought. "Actually, I do recall that the room we were in was bigger than Janus' lab. It was dark. Lights were just coming on...and there was someone there."

McKay snapped his fingers. "Yes, there was. She was laying on a table...without any clothes."

Everyone looked at him.

"What? Well, she was. I'm not making that up."

Sheppard sighed. "There was no naked woman, Rodney."

"Actually, there was." Teyla paused. "The lights were still coming on, but I saw her, too. I thought I recognized her, but then...that's when the download must have happened."

Woolsey looked at Ronon and Sheppard. "Do either of you recall seeing this woman?"

"I don't remember anything," Sheppard said vehemently.

Ronon shrugged. "I didn't see her. But I think I heard McKay say, 'Is that a naked woman?'"

"I did not!" McKay denied.

Woolsey sighed. "But you didn't see anything in this room that might give you an idea of where you were."

They all shook their heads.

"Look," Sheppard began, leaning forward, "I don't know where you think we ended up, but wherever it was, it has to be somewhere in the city. Maybe the room we were in shielded our life signs and you only thought we were no longer on Atlantis. Where else would this beam send us to?"

Woolsey nodded thoughtfully. "That is a possibility. However, our course is set back to the Pegasus Galaxy. We've tried to stop it and turn around, but we cannot change course. So we'll continue on our way until we get to wherever it is we're heading for. Perhaps once we arrive, we'll get some answers. In the meantime, I think we should see if we can locate this room here, and Dr. McKay, we have several days before we get to our destination. Do what you can to see if you can re-take control of the hyperdrive. If there is nothing else, this meeting is concluded."

As the meeting broke off, McKay was one of the first ones out the door without so much as a word to anyone. Sheppard watched him go. "What's his problem?" he asked no one in particular. "Is it just me or doesn't he seem more surly than usual?"

Teyla and Ronon exchanged looks.

"Dr. Keller's father is not doing too well," Teyla explained to Sheppard. "He was there to offer his support...but we called him back for this crisis."

Sheppard sighed. "Oh, man. And Dr. Keller isn't with us. She's still back on earth." He nodded in understanding. "That's another thing we'll have to figure out. Making contact with earth again, but we won't have any way to dial back to earth. We don't even know where we're going."

"Does it matter?" Ronon asked. "As long as it's the Pegasus Galaxy, who cares?"

Sheppard nodded toward Johanson. "He does."

Several days later, Atlantis came out of hyperspace. Sheppard was in the Chair. It wasn't that he didn't trust Beckett for this part, but he preferred to do this himself. McKay, Chuck, Zelenka, Teyla, Ronon, Woolsey, Johanson, and Patricia were in the Control Room. Two of Johanson's aides were also there, trying not to be in the way.

The second they came out of hyperspace, McKay and Zelenka discovered where they were heading for. A planet that was a pretty big blue ball, much like earth. In the Pegasus Galaxy, they were used to planets with very low population and back water technology, which usually comprised of a hoe and a rake...All of that was due to the cullings from the Wraith.

McKay and Zelenka exchanged looks.

Woolsey noticed. "What is it?"

"There's a population on this planet," McKay said softly. "At least a few million people."

"There's technology, too," Zelenka replied. "More advanced than any of the other people we've come across in this galaxy before."

"If that's true," Teyla began thoughtfully, "why haven't the Wraith culled this planet?"

McKay looked excited. "If I'm reading this right, the Wraith don't even know about this planet." He was astonished at his discovery. "It's cloaked."

"Cloaked?" Ronon pointed at the screen. "We can see it. Why wouldn't the Wraith be able to?"

"Because we are using Ancient technology. Look, there is a huge power source down there, and whatever it is, it's cloaking the entire planet from the Wraith and anyone else who doesn't have Ancient technology. That's why there hasn't been any cullings before now."

Chuck cleared his throat. "Uhm, Mr. Woolsey...we're being hailed from the planet."

Woolsey blinked. "What?" Then, he straightened his posture. "Very well. Let's hear it."

A second later, a man appeared on the screen in place of the planet. He was smiling and seemed overjoyed at making contact. Without any hesitation on his part and before anyone could speak, he said, _"People of Atlantis, it is with great pleasure that I welcome you home to the homeworld of the Ancients."_

Meanwhile, in the Chair, Sheppard was unaware of what had transpired in the Control Room. He did, however, feel as if the landing on this new planet would proceed without a hitch. He concentrated on the task at hand, filled with confidence. After all, he had done this before and under more extreme conditions than this.

Suddenly, the Chair stopped and caused him to sit up. He blinked and looked around the room. Only one thing was clear to him. The Chair had stopped working and yet he could still feel the city just breaking into the atmosphere of the planet. This was no longer a cakewalk. This was suddenly very extreme because if he didn't regain control, the city of Atlantis could very well burn up in the atmosphere.

"Ah, crap!" he exclaimed.

TO BE CONTINUED...


	2. The Descended Ones Part 2

The Descended Ones (Part 2)

_ _  
>_ Prologue _<p>

"Ah, crap!" Sheppard exclaimed, imagining that he could feel the city of Atlantis shaking all around him. If it wasn't shaking yet, it would be, or so he believed. He had been in the Chair with intentions of bringing Atlantis in for a safe landing, but that was seconds before everything abruptly stopped working. All control he originally had was gone and yet the city was still in motion, bumping against the atmosphere of the planet the mysterious hijackers had set a course for.

He tapped his ear piece impatiently. "McKay!"

_"Not now!"_ was the quick response.

Sheppard ignored him. "McKay! I've lost control of the Chair! It's not working. You'd better get down here and fix it fast or we could burn up during re-entry!"

There was no response.

"McKay! Did you just hear me?"

_"You don't have control of the Chair because the people on the planet do! The Athenians."_

Sheppard frowned. "The who?"

_"Look, there's really no time to explain. Since you're not in control, you might as well come up to the Control Room."_ There was a pause. _"You're not going to believe this."_

"I don't believe it already," he muttered. He got up from the Chair and moved toward the door. "I'm on my way."

A few minutes later, he ran past the stargate and up the stairs leading to the upper tiers. He took the steps two at a time and soon joined the growing crowd in the Control Room. No one seemed to notice his arrival. All eyes were riveted to the scene displayed on the main viewing screen in the rear of the room. On the screen, Atlantis seemed to be entering the planet's atmosphere.

Sheppard moved closer, overcome by curiosity. "How are we seeing this?"

Woolsey was standing off to the side as he watched the screen. He kept his eyes on the screen as he answered. "Courtesy of the Athenians."

"Okay...I already asked this question once, but I'll ask it again. The who?"

"Colonel, on this planet that we've been heading for are millions of people who have been thriving for many years. They have technology similar to that of the Ancients. Dr. McKay assures me that there is an immensely strong power source on the surface. That power source is assisting us in our landing."

"Really? Well, did that power source have something to do with bringing us here from earth?" Sheppard paused to consider what Woolsey had just told him. "They're called the Athenians?" He frowned. "That name sounds familiar."

Zalenka nodded from his work station. "It should. It is part of the Atlantis legend back on earth. Atlantis has also been called the Isle of Athens."

"Are you trying to tell me something?"

McKay let out a sigh. "Of course, we're trying to tell you something. We're trying to tell you that the people on this planet are claiming to be the direct descendants of the Ancients. They're telling us that their homeworld is called Athens and that Atlantis...Well, they've been expecting its return for a thousand years because this is where it originated."

"What? Wait a minute. I thought Atlantis originated on Lantea."

"We broke through!" Chuck called out. "Looks like we're heading for their ocean."

"Where else would they put us?" Zalenka asked sarcastically. "In the mountaintops?"

McKay moved around the work stations and approached Sheppard. "There's something else," he said, trying to contain his excitement. "The entire planet is cloaked. If we had arrived here in a ship without the Ancient technology, we wouldn't have seen it at all."

Sheppard looked at him, trying to comprehend what he had just heard. "Why would a planet be cloaked?"

"Probably to prevent a culling from the Wraith," Woolsey commented, aware of Johanson listening in with his complete attention.

Sheppard frowned. "But how do you even keep the Wraith from knowing there's a planet out here in the first place? You can't tell me that this planet has been cloaked for that long a period of time."

"Did we tell you about the power source we detected on the planets surface?" McKay demanded. "It's huge. In fact, I'd say there's enough power down there to supply Atlantis for a millennium."

"Are you serious?"

"Well...I will be once we get a chance to visit and see for ourselves."

Sheppard turned to Woolsey. "We're going for a visit?"

Woolsey nodded once. "If we're going to have neighbors, don't you think it would be wise to meet them? Besides, we have been invited by the Council to visit Troye and learn the purpose of why Atlantis has been called to Athens."

"Okay, but let me take my team first. We don't know who these people are."

"Agreed...but I will be going with you."

"I'm going, too," Johanson replied. "You'll need an IOA representative on this mission to keep you in check."

Sheppard glared at him. He opened his mouth to protest but was cut off.

"We'll notify Dr. Beckett as well," Woolsey decided. "I suggest we get ready and prepare a Jumper. But Colonel Sheppard..." He trailed off.

Sheppard turned to him, bracing himself. "Yeah?"

"We are not arming ourselves with weapons of any kind. This is a visit. It calls for a matter of diplomacy, not a show of force. I would like it if we could refrain from both being overly suspicious and appearing as aggressive on our return to the Pegasus Galaxy. Let's show a little trust."

"I'd advise against that."

"Duly noted. Still...no weapons."

Sheppard let out a sigh, nodded in silent resignation and turned away. He grumbled to himself all the way to the Puddle Jumper Bay.

Sheppard didn't like it one bit. It bothered him that people from the Pegasus Galaxy could hijack Atlantis all the way from earth. He didn't like it that they had used some type of a computer virus or whatever it was to take over his body to achieve their goals. He didn't like it that these Athenians could easily take full control of Atlantis and place it into their oceans with incredible ease.

One thing was abundantly clear to him. He could not trust these people. As he began to pilot the Puddle Jumper toward the city called Troye, he made a vow to himself that he wouldn't drop his guard for a second. In the Jumper, he was accompanied by his team, McKay, Teyla and Ronon. McKay rode shotgun with Teyla behind him. Ronon sat behind Sheppard. Near the back, however, there were three other passengers standing. They were Woolsey, Beckett and Johanson. Sheppard was against having Woolsey, Beckett and Johanson along for the ride. He tried to make it clear that if anything from the Athenians so much as gave him a reason to call off the visit, he fully intended to turn back.

Teyla watched him from her seat, quite concerned. She leaned toward him. "Are you alright?" she asked softly.

"Just peachy," he responded, keeping his eyes forward. "Never better."

A small knowing smile touched her lips. "You are a terrible liar."

"Yeah, well, don't worry about that. I'll work on it."

She paused, considering a different approach. "You suspect the Athenians are not who they appear to be." It was not a question.

"We've been in the Pegasus Galaxy for five years and not once have we ever come across them. We've never even heard of them until now. Am I the only one who's bothered by that?"

From the back, Ronon growled. "It bothers me."

Johanson looked puzzled. "Isn't this a part of what you people do out here?" He didn't think Sheppard had any reason to complain. "Isn't this what being out here in the Pegasus Galaxy is supposed to be about? Finding new allies to defeat the Wraith?"

Woolsey nodded his head once in response. "Yes, but that's only a part of it."

"From what I understood, finding allies was a huge part of the mission. Now you're just getting back and you have people offering help to defeat the enemy." He shook his head at Sheppard. "Why are you grumbling about a great opportunity, Colonel?"

"Because I don't like it," Sheppard snapped. "Something's not right about this. We should have brought weapons."

Woolsey shook his head. "I believe that would have been a bad idea."

Sheppard let out a sigh, frustrated. He decided not to mention the Beretta 9m he had tucked at his back. Instead, he said, "We'll see."

"Colonel Sheppard, I will lead this mission of diplomacy. However, if there is something...off once we meet our new neighbors, then you will have the authority to act. I simply must strongly advise against a violent course of action."

"Well, there isn't much to a violent course of action without weapons, but...okay. Fine. If need be...we'll improvise." He prepared the Jumper for a landing where he had received directions from the Athenians. "If worst comes to worst, we'll make a hasty retreat. Any sign of trouble, we're gone."

Woolsey nodded in agreement.

McKay leaned forward, looking out through the window in awe. "Look at that! It's like the whole city came out to see us."

Below them, people lined the streets. They were waving banners and colorful streamers. They cheered at the arrival of the people from Atlantis. A clearing was set aside for them and a group of people stood by, waiting for them. Keeping his thoughts to himself, Sheppard brought the Jumper down and made a smooth landing. Moments later, the hatch opened and Woolsey and Sheppard led the others out to meet their new neighbors. Sheppard felt naked without his P90, but the Beretta against his back was a reassuring presence.

Five people stepped forward to greet them. One of them stayed in the back wearing a long, white robe. The hood kept any features hidden. A tall man and a woman stood before the others.

The man held out his hand. "Greetings," he said, a smile on his face, "and welcome to Troye. You don't know how thrilled we are to finally meet you."

"The feeling is mutual," Woolsey said with his best diplomatic smile. He looked out over the cheering crowds. "I must admit I had not expected such a welcome as this."

"You are heroes in the Pegasus Galaxy, but forgive me. I am Darren Mace. This is Staci Coh. On behalf of the Council, we gladly welcome you to our fair city, and may we present to you someone who has been waiting for your return for several days now."

Mace and Staci stepped aside.

Sheppard, Woolsey and the others looked on with curiosity as the white robed figure stepped forward. As the person came forward, the hood fell back and revealed the face of a woman. A woman that each of those from Atlantis immediately recognized.

The woman stopped in front of them, but her eyes met with Sheppard's. She smiled warmly. "Hello, John."

Sheppard couldn't believe who was before him. The woman was Dr. Elizabeth Weir.

_ _  
>_ 1 _<p>

The George Hammond moved through the hyperspace corridor on a two-fold mission. One of those missions was all Colonel Samantha Carter could think of as she stood on the bridge, staring out the forward window. The stars streaked by at an incredible rate of speed and at any other time, she would have appreciated the beauty.

Not this time.

This time, she had no idea where that beauty would lead. Until she had discovered what had happened to Atlantis and all who were in the Lost City, she wouldn't rest. When the city had first vanished through a hyperspace window, she had wanted to go after her immediately. Unfortunately, even if she had given pursuit, she had no way of knowing exactly where Atlantis went.

The second thing that had stopped her was General Jack O' Neill's order to stand down. Pursuit was not a priority. They spent the next few days gathering key personnel and supplies. Carter had no idea why they even bothered to do that. Even if she went to the Pegasus Galaxy to look for Atlantis, it would be like looking for a needle in a haystack.

Four days after Atlantis left earth, General O' Neill not only gave the order for departure, he gave the order while on the bridge of the George Hammond. That was five days ago.

Carter still had no idea how they were going to find Atlantis...but she was also certain that O' Neill already had some ideas about that. He just hadn't shared them with her...yet.

"Are we there yet, Carter?" a voice demanded from behind her.

She turned around to find that O' Neill had entered the George Hammond's Control Room. "We should be at the drop off point in a few minutes, General," she replied. "Even if it works, sir, we still have no idea where Atlantis is to use it."

"Oh, I have an 'idea' of where Atlantis is," O' Neill said with a confident grin. "I didn't get to wear these stars on my uniforms just for my looks, you know. I also actually earned them."

Carter couldn't help it. She grinned back at him. "How long will you be staying there?"

"Just long enough to make sure it's operational. Then, it's back to the SGC. I'll be home before you will, cooking up some fish and watching reruns of The Simpsons."

"General, are you going to tell me your idea about where Atlantis is?"

"Sure, I will." He paused for affect. "It's in the Pegasus Galaxy." He waved a hand in the air for emphasis. "Somewhere...that a-way."

Carter regarded him with a look. "How can we even be certain of that, sir? For all we know, they could be any where. Maybe they didn't go to the Pegasus Galaxy."

O' Neill nodded thoughtfully. "Oh, I'm sure they went to Pegasus, Carter. Whatever it was that affected Atlantis and caused it to leave earth, I'm sure it originated there. Once you get there, you'll see." He smiled. "You'll figure it out."

"You're going to have to tell me before you leave. You might as well tell me now."

O' Neill looked at her.

Carter waited.

"You always could spoil the fun out of a surprise, Carter," he told her. "Did you know that?"

"I thought you didn't like surprises."

"I don't, but I sure as hell love to give them."

Having reached their first destination, the George Hammond dropped out of hyperspace. O' Neill shared his idea with Carter before he and the newly assigned personnel left the ship. When she heard the idea, she realized that she should have known what was coming next.

He couldn't believe it. Not again.

Elizabeth Weir had almost died in an explosion during an attack on the city by the Wraith. If it hadn't been for nanites, she would have died then. Then, the replicators took her when McKay revived a command into the collective that caused them to concentrate on destroying the Wraith. And finally, Weir herself led a small band of replicators to their deaths by stepping through the stargate...and out into deep space.

Atlantis had lost her three times.

They weren't going to lose her again.

He wasn't going to lose her again.

It looked like Elizabeth Weir. It sounded like Elizabeth Weir. Sheppard was more than convinced it wasn't Elizabeth Weir. He had said that if there was any sign of trouble, they would immediately head back to Atlantis. He had no doubt in his mind that this was definitely trouble.

"Everybody back to the jumper!" he snapped, turning abruptly away from the imposter and the Athens. "We're leaving now!"

Woolsey stepped into his path. "Colonel, I seriously doubt this is the trouble we talked about."

Sheppard glared at him. "Look, I'm telling you there's something wrong here! You've got to trust me on this."

Woolsey hesitated. Finally, he nodded.

_"John!"_ Elizabeth exclaimed. _"Please!"_

Sheppard deliberately ignored her. He was the first one back inside the jumper. By the time everyone was inside and as the hatch was closing, he aimed it for the skies.

Teyla, Ronon and McKay had taken their seats, but they kept their own thoughts to themselves. At least for the moment. Their silence only showed that they had not been prepared for seeing someone who they thought was dead. Especially someone they had loved. Like Sheppard, they were trying to process it.

Once they were on their way back toward Atlantis, Johanson had to be the first to speak. "Would someone please tell me what _that_ was all about?"

Sheppard and his team remained silent while Beckett and Woolsey exchanged looks.

"Don't leave me in the dark here," Johanson warned. "I'll find out anyway, but I'd prefer it if you told me now."

Beckett scowled. "Are you daft? That woman down there was _Elizabeth Weir,_ which should not even be possible. You're IOA, aren't you? I'm sure you must have seen plenty of reports come across your desk that concerned Dr. Weir."

Understanding dawned on him. He nodded slowly once. "I see." He watched the others, studying their reactions. "I'm still not quite sure I get it. You all obviously care fro the woman, or did at one time. I would have thought you'd be happy to see her alive and well."

"You're right," Sheppard agreed. "You don't get it."

"How about clueing me in?"

"It's none of your business."

"I disagree. Clearly, this unexpected turn of events is likely to affect your judgement. From what I'm seeing, you should have some quality down time until the matter can be resolved."

Ronon shook his head with a grunt. "It's a good thing that's not your call to make."

Johanson opened his mouth to respond.

Woolsey beat him to it. "That may be so, Ronon. However, it is my call to make."

"What are you saying?" McKay wanted to know. "Are you shutting us down? I've still got to figure out what got us here in the first place. We didn't even get to find out where the power source is because I'm telling you, something here was powerful enough to bring us right to this planet! There is something seriously wrong here! You can't shut us down."

He shook his head. "I don't intend to."

McKay hesitated. "Oh...you don't?"

"No, I don't." Woolsey paused. "But since...your possession, and with all that's been happening, we neglected to have you examined in the infirmary. When we get back, Dr. Beckett, I would like you to take care of that right away."

Beckett nodded once. "Of course."

"While that is being done, I'll make arrangements for another meeting with Darren Mace, Staci Coh and...Dr. Weir." Before Sheppard could protest, he said, "Like it or not, there are still answers we need and the only way to get them is to meet."

"Oh, no..." McKay said softly as he came to a sudden realization.

Teyla turned to look at him. She had come to the same realization.

"What?" Sheppard growled.

McKay suddenly averted his eyes and looked away. "Nothing."

"Then, why did you say _'Oh, no'_? Usually when you say that, something's about to blow up or we're about to be killed."

"I didn't say that. Nothing's going to blow up. There's nothing wrong. Absolutely nothing wrong at all."

Teyla cleared her throat. "Rodney thinks that the woman we saw before we were taken over was Dr. Weir."

McKay swallowed. "No, I don't! Not really. I'm one hundred percent positive it was somebody else!"

Ronon blinked. "Wait a minute. The naked woman you saw after that first bright flash...was Dr. Weir?"

"I didn't say that!" McKay protested. "I never said that at all!"

"But it _was_ Dr. Weir," Teyla confirmed.

"Okay, now...you see, I'm not convinced that I saw a naked woman at all. Period! I certainly did not see Elizabeth like that because if I did - and I strongly stress that I didn't - but if I did, I assure you that I have absolutely no memory of it! At all!"

Sheppard let out a sigh. "Rodney."

"Wherever that bright flash took us, it was dark. I mean the lights were gradually coming on, and before they were all on, I saw...the woman."

"McKay..."

McKay waved his hands as he spoke. "Okay, I suppose it could have been Elizabeth, but I couldn't really tell. I mean, it's not like I've ever seen her naked before...because I haven't! I really really haven't!" He swallowed. "I didn't see a lot. Much." He closed his eyes. "Oh, no."

"McKay!" Sheppard snapped impatiently.

McKay turned to him. "What?"

Sheppard paused as he looked out at Atlantis as they approached. Then, he let out another sigh. "Okay...Teyla. Rodney. I want you both to think about this. As I recall, wherever the hell that bright flash took us, Ronon and I didn't see any woman, naked or otherwise. We had our attention focused on the other side of the room. What I'm going to ask you is this...Can you be absolutely certain that the woman you saw was...was Elizabeth?"

McKay swallowed again. "No...?"

Teyla paused. "I believe it is possible that it could have been."

"Do you have any idea what you're saying?" Sheppard demanded. "You're suggesting that the bright flash which took us from Janus' lab brought us all the way to here...on Athens. From earth. To the Pegasus Galaxy from the milky way. Now I ask you...if that is what happened, how is that even possible?"

No one had an answer.

Elizabeth Weir helplessly stood by as she watched the jumper fly away. She balled her hands into fists at her sides and felt the tears of frustration and loneliness begin to fill her eyes. They had been so close...but still so very far away. Now maybe even farther than ever.

Staci came to stand at her side. She placed a hand at the small of Elizabeth's back as an offer of comfort. "Elizabeth," she said softly, "I'm so sorry. I know this wasn't the reunion you were hoping for."

"No," Elizabeth said bitterly, trying to reign in her emotions. "It wasn't."

"Perhaps they're just not ready," Mace offered gently. "Perhaps it was too much to hope for that they would simply accept you back. You've all been through so much."

"I should have stayed in the lab where you found me." Elizabeth paused as she took a few steps forward, as if she could move closer to Atlantis. She wondered if there was ever a chance that she could call it home again. "I should have let you bring them to me like you've suggested. I was just so excited. I -" She took a deep breath. "I wasn't expecting this, but I should have."

"They don't know that it's really you."

Elizabeth closed her eyes. "Maybe that's the problem, Darren. I'm not sure either that it's really me."

Zelenka had run enough diagnosis' on every system in the Control Room of Atlantis, he felt like his head was about to explode. He had been hard at work trying to find out how the controls had been taken from the Chair and diverted to the planet. He wanted to prevent such a thing from occurring again. He thought that maybe the answer was somewhere in Janus' lab. However, he dreaded the thought of going in there and yet if he didn't look into it soon, McKay would have his head on a silver platter.

He hoped he wouldn't open up any other surprises for they certainly had more than enough. That Janus was a sneaky son-of-a-gun. As Zelenka headed down the steps from the Control Room, he happened to see Patricia Manor and Doreen Stills standing in front to the stargate. They appeared to be arguing, but they stopped as he approached them.

"Is there something wrong?" he asked, not really caring one way or the other. The women were, after all, IOA.

"No," Patricia responded sharply.

Doreen's answer, however, was just the opposite. "Jed and Cheryl are missing."

Zelenka paused to regard them both. He looked at Patricia. "To you, there seems to be nothing wrong." He turned to Doreen. "Yet you say your fellow interns are missing."

"Two of them are, yes."

Patricia sighed. "They obviously evacuated from the city before we left earth."

Doreen shook her head. "No. I don't think so. Jed and I had breakfast with Teyla a few days ago and that was when we were traveling through space. And another thing, Cheryl and Jed aren't the only ones missing. A few other interns are missing as well."

"How many others?" Zelenka asked.

"Four."

He blinked. "Four? So...that's six interns believed to be missing?"

"Yes," Doreen said.

"No," Patricia replied sharply.

Zelenka frowned. "Exactly how many interns does it take to...?" He shook his head. "Never mind. I'm sure you would not appreciate the joke. How many interns did you and Mr. Johanson bring onto Atlantis?"

"Including myself," Doreen answered before Patricia could, "twelve."

"Really? Twelve? That's a bit excessive, isn't it?"

Patricia looked at him, her hands on her hips. "We take our work very seriously."

Zelenka nodded once. "I'm sure you do. However, the disappearance of six of your _seriously_ working interns I think raises some alarms. If you cannot account for them having been evacuated before we left, this could be a problem. I believe we should bring this to Major Lorne's attention immediately."

At the same time, Doreen said, "Thank you." And Patricia replied, "That won't be necessary." Then, the two women glared at one another.

"Perhaps it isn't necessary," Zelenka assured Patricia, "but it wouldn't hurt to mention this to Major Lorne, would it?"

Patricia relented with a nod. "No. It wouldn't."

"Then, let's go find him, shall we?"

Once they had returned to Atlantis, Woolsey headed directly for his office. Johanson was right at his side, a continual thorn that refused to go away. Something, however, captured Johanson's attention and caused him to walk away. Woolsey had no idea what it was, but he was grateful for it.

In his office, he arranged to contact the Athens and because of the state-of-the-art technology, combined with the Ancient technology, he was able to communicate directly with Darren Mace through his laptop.

"First and foremost," Woolsey said after they greeted one another, "I would like to apologize for our abrupt departure. It seems that there was a most unexpected...development that caused us to re-evaluate our situation."

On the laptop's monitor screen, Mace nodded in understanding. "Dr. Elizabeth Weir."

Woolsey confirmed it with a brisk nod. "We...would like to try this again, but under a few conditions."

"Of course. I assure you, Richard. Our intentions for you and your people are for the good. We wish you no harm."

"And yet you've somehow managed to hijack us here from our galaxy to yours." He spread his hands. "Surely, you can understand our suspicions."

Mace held up a hand. "While I do fully understand your position, I assure you...we had nothing to do with what brought you here."

Woolsey sat back. "Really?"

"I tell you a truth. We can help you determine what brought you here, but we are not the cause of it. Richard, I can tell you that what brought you here is the same thing responsible for Elizabeth's arrival as well."

Woolsey could not come up with a response.

_ _  
>_ 2 _<p>

Sheppard had wanted to return to the Pegasus Galaxy, but not like this. Hijacked from earth by some type of weird mind control or, as McKay had explained it, a virus download directly into the brain. Yet there they were, back in the Pegasus Galaxy. They wound up on a planet inhabited by people who claimed to be direct descendants of the Ancestors. To top all of that off...who decided to show up?

Elizabeth Weir.

Her arrival should not have even been a possibility. Sheppard had almost come to accept that she was gone. Now he found himself fighting against feelings he didn't want to revisit. He stood in the infirmary waiting for his examination with his arms folded across his chest and his eyes glaring straight at the wall across the room.

McKay sat in a chair, also waiting for his examination. He let out a loud sigh. "No matter which galaxy you wind up in," he began, "ever doctor's office is always the same. You always have to wait." He suddenly sat up. "Of course, the lollipop at the end of the visit was always worth the trip. Or at least_almost_ always worth the trip. Everybody loves a lollipop. My favorites are the orange and the yellow, but definitely orange." He paused. "I don't suppose Carson even has lollipops, but Jennifer did. She...always had lollipops." Suddenly, he fell silent.

Sheppard frowned. He snapped out of his own thoughts and forced himself to look at McKay. It suddenly occurred to him that the super genius scientist did not look happy at all.

"Rodney," he said hesitantly, "I'm sorry. Throughout all the fun we've been having, I forgot that you and Dr. Keller were..." He trailed off. Then, he sighed. "We're not done here. We'll figure things out, re-establish contact with earth and get Dr. Keller back here."

"She didn't want to come back," McKay said softly. "Come to think of it, neither did I."

"What are you talking about? Of course, you wanted to come back here. We all did. Not like this, but we did want to return."

"You don't understand. Without Jennifer being here...I don't want to be here without her."

"I told you, we'll get her back."

McKay turned to look at her. "Her father is dying and...and I can't be there for her! Do you have any idea how that makes me feel? Don't you think I know how I am? Jennifer is the only one who fully accepts me for the way I am. She...she looks past all of the arrogance and the oh so many short comings that I have...and she looks right at me. You know what? Her father did, too, come to think of it. He looked past all of the junk and saw me." He stood up and swallowed. "They accepted me, junk and all. No one has ever done that. Not Kate. Not Carson or Zelenka. Not Teyla, Ronon...Not even you. For the first time in my life, I have a connection and I don't want to lose it. I don't want to lose Jennifer."

Sheppard was stunned. For the first time since he had known McKay, he thought he was seeing a new side of him he never knew existed. A new Rodney McKay. When he found his voice, he said, "I'm sorry, Rodney. I...I knew you were seeing each other, but I really had no idea it was this serious."

"Be honest. You didn't think it was serious because you didn't believe a guy like me could have a woman like Jennifer fall for me." He watched Sheppard. "Did you?"

Sheppard cleared his throat. "To be honest...?"

"Go on," McKay prodded.

Sheppard let out a breath. "Okay. No, I didn't think that Dr. Keller...or any woman for that matter, could ever fall for a guy like you."

McKay began to nod. "I thought so." The rest of what Sheppard had said began to sink in. "What do you mean by any woman for that matter?"

"Nothing." He shrugged. "Forget it."

Mckay frowned. Finally, he nodded slowly and sat back down. "It's okay. Like I said, I know how I am. Being with Jennifer...Well, she helps me see things I haven't seen before. About myself. About others, too."

There was a pause.

"Rodney..."

McKay turned his head. "Yeah?"

"For what it's worth...you're not just a part of the team." He paused because he was not used to expressing his personal feelings to anyone. "You're family," he finally said. Then, to lighten the mood and break the tension, he added, "And you also saw Elizabeth - or whoever that woman was - naked."

"Stop reminding me of that!" McKay snapped. "I'm trying to forget!"

"I'll bet that won't be easy."

"Not if you and Ronon keep reminding me every chance you get, it won't!"

Sheppard couldn't help it. "Do you really want to forget?"

McKay hesitated. "What? Yes! Of course, I want to forget, but you're really not helping!"

Sheppard grinned. Knowing he could still get McKay worked up improved his mood greatly.

Ronon was not the most patient guy there was, but somehow he made himself endure the physical examination. Dr. Beckett ran him through the paces, taking his time because he wanted to be sure there was nothing wrong. There did not appear to be, but he had come to discover that on Atlantis, nothing was ever what it appeared to be.

"All right, Ronon," he said as he looked at a monitor on a rolling stand. "Your heart rate and blood pressure are as it should be. You're as healthy as a horse. Not a bloody thing wrong with you."

Ronon shrugged as if he didn't have a care in the world. "I didn't think there was to begin with."

"I'm sure Mr. Woolsey will be happy to hear it as well, but first, I've got to run Dr. McKay, Colonel Sheppard and Teyla through as well. I expect to find the same results."

Ronon got to his feet. "That's it, then?"

"That's it."

The Setadan, however, didn't leave. "Do you think that was really her?"

"Elizabeth, you mean?" Beckett paused to consider his answer. "Without a complete examination, I can't be sure. We all thought she was dead, Ronon. For all I know, that's a replicator." He paused again as he considered another possibility. "Or she could be a clone...like me."

Ronon regarded him. "If she is a clone, she'd be able to come back then, like you did. Wouldn't she?"

Beckett hesitated. "If she is a clone, then how did she come to be? Who's responsible and for what purpose? We still don't know anything about the people on this planet, but we do know that they brought us here by taking over your minds and hijacking Atlantis. We really can't be certain then of who that woman is until we know who they are."

Ronon shrugged. "All I know is that the woman looked exactly like Elizabeth Weir and sounded like her, too. So maybe...just maybe it _is_ Elizabeth Weir."

"That's wishful thinking, lad."

"Yeah? Well...so were you."

Beckett didn't know how to respond to that as he watched Ronon walk out of the infirmary.

"What right did you have of alerting the military presence that my interns may have disappeared without coming to see me first?"

Doreen hesitated. She had seen Johanson angry before, but this time was different. He looked mad enough to commit murder. She saw it in his eyes and it scared her. "I did what I thought was the right thing to do," she responded defensively. "They are missing and you weren't here for me to bring it to your attention."

"I'm here now. You could have waited, or you should have at least talked it over with Patricia."

"I did talk to Miss Manor."

"What did she say?"

"She seems to think that nothing's wrong. That they might have gotten off Atlantis before we left earth but-"

Johanson glared at her, interrupting. "That seems logical enough to me."

Doreen sighed. "It would...if I hadn't seen some of them during our trip through space. You can be angry all you want. Something's wrong. They didn't just disappear. Something happened to them and Major Lorne assured us that he would find out what did happen."

Johanson reigned in his anger as he turned away from Doreen. He saw the two marines he had assigned to him, hanging back on the terrace to give them space. The IOA representative took a moment to calm himself. If he didn't, he would be dangerously close to picking up Doreen and tossing her over the side. He would like to do that to Patricia as well. She had joined Major Lorne's team for the search.

When he turned back around, he saw that Doreen was watching him with suspicion in her eyes. He realized he had to be careful. She was a smart girl. Perhaps too smart for her own damned good.

"What did you do?" she finally asked.

A feral grin appeared on his lips. "What did I do?"

"You did something."

"What do you think I did, Doreen? Are you saying I'm responsible for their disappearances? You should be very careful about making accusations when you have no evidence to support your claims."

Doreen glared at him. "I don't know what happened to them, but I'm sure that you do. Whether you're responsible or not, you know something. You're hiding something. Why don't you just tell me?" She looked into his eyes. "Will Major Lorne find them? Are they even on Atlantis?"

"You know what? You ask too many questions."

"I'm going to keep asking until I get answers."

Johanson paused for a moment. He let out a sigh as he stood by the balcony, looking out at the alien ocean below. His trusted men continued to hang back and out of sight. Finally, he gestured for her to approach him.

Hesitantly, Doreen approached him and leaned on the balcony beside him. She didn't say anything. She decided to wait.

The wait wasn't long. "Who do you think you are?" Johanson demanded, bringing his face closer to hers. "You are under my authority. Not above it. You are going to drop this or I am going to drop you. Are we clear?"

She swallowed and backed away. "I...I'm not questioning your authority. I just...I'm worried about my friends."

"Your friends are doing their jobs."

"What?"

"They're doing what they've been ordered to do. They're investigating everyone who was a part of this expedition. Unfortunately, you've just interfered with that by bringing it to Major Lorne's attention. If they find them, our investigation is over." He leaned toward her. "Thanks to you."

Doreen let out a sigh, horrified at what she had done. "I'm sorry. I didn't know."

"You didn't know because you weren't supposed to."

She paused. "So...they're still here, then? On Atlantis? Why haven't I seen them?"

"Oh, you want to see them, do you?"

She nodded. "I do."

"Fine. I'll take you to them...and then we can consider this matter closed."

She nodded in agreement.

He took her by the arm and led her to where she would get the answers to the questions she had been asking. Those answers, however, were not answers she was going to want to hear.

It was time. The physical examinations of Colonel Sheppard and his team had been completed. There were no residual affects since after the hijacking. They were back on full duty and ordered to the jumper bay to meet their guests. The Athenians arrived via a jumper of their own, but their jumper seemed to be longer and more rounded on the edges.

Sheppard actually let out a whistle of appreciation as he saw it come into the bay.

Woolsey turned his head. "I have to agree, Colonel. That is an impressive jumper."

Sheppard nodded slowly. "It's a luxury jumper, with all the accouterments."

McKay frowned. "Accouterments? Who says 'accouterments'?"

"Apparently," Teyla replied with a smile, "John does."

They all fell silent and waited as the luxury jumper landed in the bay. Then, they gathered at the hatch to wait for it to open. The hatch rose up and a ramp extended downward. Inside the jumper, there were two pilots, Darren Mace, Staci Coh...and Elizabeth Weir. They each came out of the jumper and made their approach.

This time, Elizabeth didn't speak but her eyes searched the faces Sheppard and the others carefully. Sheppard tried hard not to look at her. He refused to believe it was her.

Woolsey did all the talking this time. He introduced Colonel Sheppard and his team, Dr. Beckett and Patricia Manor, who was attending the greeting process instead of Johanson. Patricia was stunned when she saw Elizabeth. She kept watching her and occasionally, she cast a suspicious look at Sheppard as if he had something to do with Elizabeth's mysterious return.

For the most part, Sheppard ignored her presence as well.

After the introductions, Woolsey turned to Elizabeth. "Dr. Weir...as much as I would like to say that it is a pleasure to see you again, I hope you can understand our caution."

Elizabeth looked at him and nodded. "I do understand. If our places were reversed, I'd be just as cautious." She was aware that McKay, Ronon and Teyla were watching her closely. It hurt her that Sheppard wasn't. "I want to assure all of you that I will do whatever it takes to ease your minds."

McKay couldn't remain silent any longer. "How...how is this even possible? Are you really Elizabeth? You were dead. We saw you-"

"McKay," Sheppard snapped. But he said no more. His tone should have been enough.

And it was.

McKay closed his mouth and didn't say any more.

Elizabeth regarded them carefully. "You want to know why I'm here and if I'm even the Elizabeth Weir you once knew." That familiar tug of a half smile they were all used to tugged at her lips. "The irony is...I want to know the same thing." She looked at Beckett. "That's where you come in."

Beckett nodded at her reassuringly. "I'm all set to give you a thorough examination, Elizabeth. If you're not who you appear to be, I'll know."

"And if she is?" Ronon inquired.

"Then, I'll know that, too." He held out his hand, gesturing to Elizabeth. "If you'll come with me, then...?"

She nodded slightly. "Of course."

Everyone but Sheppard watched them walk away. Sheppard nodded silently to the two guards he had assigned to keep an eye on their new visitor. He felt a lot better when the two men fell into step behind Beckett and Elizabeth.

Teyla looked at Sheppard, frowning.

Sheppard focused his attention on Mace and Staci.

"Alright then," Woolsey began, putting his hands together. "Why don't we take our places at the conference room and get to know one another?"

"Of course," Mace responded with a nod.

"Then, right this way," Woolsey said as he led the way.

Zelenka and a few other scientists were at work in Janus' lab, trying to find out how Atlantis was hijacked and how to prevent such a thing from happening again. One way to do that was to purge every system in the lab. Unfortunately, that option could also delete valuable data from Janus' computers. Since they had discovered the lab due to the help of Dr. Daniel Jackson, there had not been enough time to go over everything.

They were now past the point of making up for that time.

As Zelenka was running a complete diagnosis on vital systems, he was trying to view some of the files Janus had been keeping. Unfortunately, they were all encrypted. None of the files would even open even if they weren't encrypted.

"That was her!" someone exclaimed, shaking his head in awe as he entered the lab with a coworker. "I'm telling you, that was really her!"

The coworker shook her head. "I don't think so, Tony. That's just not possible. We know she died going through the wormhole with those other replicators, and even then, that was her consciousness downloaded into a replicator. So basically, she really has been dead longer than that. Anyway, that woman right now visiting our city is just a look-a-like or something else. I'm telling you, we need to get off this planet as soon as possible. Something is not right here."

"But that looks exactly like her. Even sounds just like her. She said hello to me when we passed them in the hall. Come on! How can you say it's not her, Kate? We've seen a lot of other unexplained things happening while on Atlantis. Why not this? Radek, what do you think?"

Zelenka didn't even look at him. "I think we have a lot of work to do before we can even entertain the possibility of leaving this planet."

"Yes, but Dr. Elizabeth Weir-"

"-Is not our priority. I expect you to focus your attentions on what is."

Kate and Tony exchanged looks, but they went to their workstations and got into their work. At an unoccupied workstation, a small red light suddenly flashed three times rapidly on a control panel. Then, the light became steady until it finally turned off. No one had noticed it.

In space, however, a black ship entered into the system and came to a stop.

Johanson showed up just before the meeting officially started. "I had matters to attend to," he said by way of offering up an excuse. As he took his seat, Woolsey introduced him to Mace and Staci and informed him that Dr. Beckett had taken Elizabeth Weir to the infirmary. Johanson glanced at Patricia and received a nod for confirmation.

"Now," Woolsey began as he sat back with his hands on the table, "let's talk, shall we? I'm sure that you have just as many questions about us as we have of you."

"Actually, we know a lot about you," Staci replied with a smile. She looked at Sheppard and his team with admiration. "We know that you're hero's of the Pegasus Galaxy, saving countless lives from the Wraith. When we learned that you were no longer with us, we lost all hope." She turned to look into Woolsey's eyes. "But then you came back. You've returned and our hope was restored."

Sheppard let out a sigh. "Yeah, about that. It's not that we didn't want to return, but being hijacked was not how I pictured it happening."

Mace leaned forward. "Please understand, Colonel Sheppard, that how you were brought back was not our doing." He paused. "I have already given assurances to Richard concerning the matter. You have absolutely no reason to fear us. We are your friends. Our world is your world. After all, we are brothers, are we not? Are we not all descendants to the Ancestors?"

"That all sounds good, but I'd like to see those assurances first hand before I make any conclusions."

"Of course. Anything you require, it will be done."

Before anyone else could say a word, Woolsey spoke up. "Can you tell us if you know how we got here?"

Staci smiled. "Yes. We do know how you got here." She exchanged knowing looks with Mace. "It was the Ancestors. They brought you here...Just as they brought Elizabeth Weir."

_ _  
>_ 3 _<p>

"You're saying the Ancestors," Sheppard began, clearly doubting what they had just been told, "the Ancients themselves are solely responsible for not only our return to the Pegasus Galaxy...but also for the woman's return as well?"

Mace nodded. "I am."

"I don't understand." Staci frowned as she regarded Sheppard. "Elizabeth is your friend, yet you treat her like an unwelcome guest."

"Look, I only know that _that_ woman who came with you claims to be Elizabeth Weir." Sheppard made eye contact with both Mace and Staci, trying to stress his side of things. "I'm not just going to take her word for it, or yours."

Mace let out a small sigh. "I truly regret that we cannot get you to believe the truth. Perhaps in time, you _will_ see us as friends that you can trust."

Woolsey opened his mouth to respond.

Mace held up his hand, halting him. "We understand your resistance. We know what you've been through and know that you do have plenty of reasons to be suspicious. But there is also a lot of things you do not know. In your absence, the Wraith have reasserted themselves as a power to be reckoned with. Worlds that you have helped in the past have been annihilated. The Coalition and the Genii have done all they can to turn the tide...but they are losing."

"What are you doing to help them?" Ronon asked.

Johanson sat back in his chair as he glanced at Patricia. He remained silent, taking everything in.

Mace and Staci exchanged looks.

Sheppard and Woolsey did, too. Sheppard's look told Woolsey that he had no intention of trusting these people whatsoever.

"Are you able to help?" Teyla inquired, always the diplomat.

"We are training an army to fight the Wraith," Mace finally said.

Sheppard glared. "Training?"

Mace nodded.

"Please, you must understand," Staci pleaded. "We have been at peace for a thousand years."

"A thousand years?" Sheppard couldn't believe what he was hearing. "You've been on this planet - a planet that has been cloaked - for a thousand years? You know about the Wraith and what they're doing and have done nothing to help? How do you expect us to trust you?"

"It's not that simple. The Ancestors placed us on this world for our very survival," Mace tried to explain.

McKay frowned at that. "But you said for a thousand years. We know that this war has been going on for longer than that. The Ancestors left Atlantis millions of years ago, ergo if they are the ones who placed you on this planet, how do you account for such a large gap? What happened to the rest of your history?"

Staci turned to him. "It was destroyed by war."

"Before the thousand year peace," Mace said, "our planet had been ravaged by war. We nearly wiped our very existence out, but some hid underground. When they were able to come back out, they started over. They rebuilt our world into what it is today and we have been at peace for a thousand years."

"This war didn't do anything to the...cloak?" McKay asked.

"The Ancestors have shielded the power source of the cloak from any attempt to disrupt it."

"So...no one's ever even seen it?"

"That's correct." Mace paused. "We survived a war with ourselves a thousand years ago." He glanced at Staci. "Before that, our Ancestors did not want to become an extinct race themselves so with great effort, they placed aside a remnant to survive the attack from the Wraith. They made a way by using great power to shield the very existence of our world from the Wraith. They did this, then they told us that they would make a way for them to return to us, or if not them, then their descendants...like us. They promised that you would return to us in the Lost City. Upon your return, we have been promised that the end of the Wraith would soon follow."

Staci smiled at Woolsey. "We have been waiting for this day to come. Now that we know you're here, we believe the Wraith will soon fall." She looked at the others. "Elizabeth is a part of this. We know she died by sacrificing her own life to save yours from the Asurans. We believe that at her death, she ascended. Now, she has returned. A secret lab under the City of Troye alerted us to her arrival here."

McKay sat up. "Did you say a secret lab?"

Mace nodded once. "Yes. We had no idea of its existence, but as soon as Elizabeth arrived in the lab, a beacon began to emit. That's how we were able to find the lab."

"When you say that Elizabeth arrived," Woolsey began, "what exactly do you mean?"

"We know she simply just appeared. She was on a lab table when we found her." He looked closely at Sheppard, Teyla, Ronon and McKay. "You should know this. You were all there. Monitors from the lab reveal that not long after Elizabeth appeared, then so did you four."

"What?" Johansons exclaimed.

"That isn't possible!" McKay exclaimed. "We were on earth, which is a lot farther than you can imagine. I can't even comprehend how traveling through space from one galaxy to another without a ship or a wormhole can be done!"

"Nonetheless," Mace assured him, "that is what happened. She arrived. Then, you arrived. Moments later, you vanished. We were able to determine that you had returned to your own galaxy to bring Atlantis here."

"Do you know anything else about this lab?" Woolsey inquired. "Like who it belonged to?"

"Elizabeth believes it was once used by someone named...Janus."

Woolsey nodded slowly. "We are familiar with Janus."

"Who does this guy think he is?" McKay snapped. "I swear, this man has a lab in every port!"

"Does that bother you?" Ronon asked.

Sheppard snorted. "Of course, it bothers him because he doesn't have a lab in every port."

"I'm happy with the lab I have," Mckay protested. "With too many labs, you'd be stretched out all over the place. Nothing would be centralized and they would be open for any one to just go right in and take it!"

"Janus' lab, as I recall," Woolsey began, "wasn't exactly open."

"Well...maybe not for you, but it didn't take me long to get inside."

Teyla tried not to smile, amused. "Didn't Dr. Daniel Jackson help you with that, Rodney?"

McKay blinked. "Oh. Yes. Of course. A little. Didn't I mention him?"

"I thought Dr. Jackson was the one who knew about the lab before you did," Ronon couldn't help but point out.

"That may very well be...but I would have found it anyway sooner or later." He turned to Mace and Staci. "This lab is under your city?...Troye?"

They both nodded.

"It is," Mace confirmed.

"I wonder if it is identical to the one we discovered." McKay paused deep in thought. "Something there used an awful lot of energy to transport us back and forth. I'd like to see this lab."

"Of course."

"I'd also like to look at the power source behind your cloaking technology."

Mace and Staci exchanged looks again.

McKay noticed. "Is that a problem?"

Mace shrugged helplessly. "We don't know how to get into the relay stations. Our world has always been cloaked, even during the war, but in all that time, Dr. McKay, we have never been able to gain entrance."

"There are four stations," Staci replied. "Each of them are positioned just so...North, South, East and West. Once, our people had tried to get inside, just to see what it was like...but they had failed. Now...those stations are mostly disguised by the very elements."

Woolsey turned his head. "Perhaps now would not be a good time to look into those relay stations," he said to McKay. "For now, we should focus our attention on the labs."

McKay nodded, but he was sorely disappointed.

"So your people have no idea what is powering the cloak?" Patricia inquired.

Mace and Staci both shook their heads.

"But you've thrived for a thousand years. You've built cities. You do have technology. And you are aware of what is happening in your galaxy. How? Do you have a stargate?"

Sheppard and Teyla exchanged looks. He couldn't believe that someone from the IOA would actually ask a good question.

Mace shook his head. "No. We do not have a stargate. We do, however, have a friend who visits from time to time. He shares information with us and we offer him friendship and hospitality."

"Who is this friend?" Sheppard asked. "Anyone we know?"

"His name is Lenox," Staci replied softly.

Teyla regarded Staci. "How did you come to be friends with Lenox?"

Staci didn't answer and she made no eye contact.

Mace glanced at her as he leaned forward. "He crashed his ship on our planet as he was pursued by the Wraith. He was at death's door when he was found, but help came to him quickly. He was brought to our hospital in Troye where he eventually recovered."

"His wounds were quite severe," Staci added thoughtfully. "During the surgery, we discovered that a device had been implanted to his spine. Removing it had almost killed him..." She swallowed as if reliving a memory she didn't want to. Then, she recovered. "...but as Darren said, he did recover."

McKay blinked. "A runner! You're talking about a runner!"

Sheppard, Teyla and Woolsey turned to look at Ronon.

Ronon simply shrugged, knowing what they wanted to ask. "Never heard of him, but it's nice to know another runner is free."

"Did the Wraith ever come here looking for him?" Woolsey asked.

Mace nodded. "They did. However, since they could not detect our world, they flew their ships in space searching for any sign of Lenox and his ship. After the device had been destroyed, they left our system. That was several years ago. Lenox has been our friend ever since." He exchanged a knowing look with Staci. "He used to come to us every other month to share information with us about what has been happening. He shared stories of your battles against the Wraith; your successes and your failures."

"Well," Sheppard began casually, "we try not to focus too much on our failures."

Woolsey regarded the Athens. "When was the last time you've had contact with this Lenox?"

"Four months ago." Staci couldn't hide her concern which she felt for Lenox. "That was when we were told about how the Wraith were winning the war against the humans in our galaxy. He...promised to return to us again after a mission he was involved in was over." She looked at the surface of the table and swallowed. "He has not yet returned.

Teyla watched her for a moment. Staci looked up from the table and into her eyes. Then, she quickly looked away.

"What mission?" Ronon asked.

Staci paused. "He didn't say."

Ronon regarded her for a moment. "If you're worried about him, don't be. He's a runner. He can take care of himself."

"Thank you," she said softly.

"You're welcome."

Johanson frowned at Ronon. "They just told us they took the device out of him. He's no longer a runner and neither are you."

Ronon shrugged. "Once a runner, always a runner. Without the device, we're just runners with more freedom. But we're still runners."

The IOA man just looked at him.

Everyone fell into silence, taking a moment to reflect on what had just been discussed.

"Well," Sheppard finally said, "now that we know a little more...we need to come up with a plan."

Woolsey nodded his head. "Agreed. Dr. McKay, you will need a team to check out the lab discovered under the City of Troye. Coordinate with Dr. Zelenka. Maybe the two of you can find out what got us here in the first place."

Sheppard scowled. "Find out what took control of us and make sure it doesn't happen again."

"Sure. No problem." McKay sat back in his chair. "Piece of cake."

"Meanwhile," Woolsey continued, "I'll have Chuck assemble another team to work on getting the stargate operational once we can correlate the new point of origin. We'll need to begin re-establishing our own presence in this galaxy and make contact with what allies we still have. And somehow, we'll have to find a way to contact the SGC back on earth."

"Easier said than done," Sheppard replied.

Woolsey turned to their guests. "This army you were talking about...How far have they come in their training?"

"We've begun training once we heard that Atlantis had risen again," Mace responded. "That was five years ago."

"How big is this army?" Ronon asked.

"Ten thousand strong," Mace answered proudly. "With hundreds more enlisting every day."

Staci smiled. "Our people want to get into the fight. We have been preparing ourselves. So please...Trust us. Use us. Let us now do our part."

Sheppard looked at Woolsey.

"We do appreciate your gracious offer," Woolsey assured them, "and we certainly will take it into deep consideration. I can't imagine going up against the Wraith with ten thousand soldiers, but that certainly increases the odds on our side."

"Yeah, sure. Ten thousand soldiers. On the ground. Easy pickings for a culling."

Mace and Staci exchanged looks again, each of them smiling.

"There is something else," Mace began carefully. "We've also had our best engineers at work for several years, even before we learned of Atlantis' rising. At first, we were designing them for simple exploration. When we heard of your fight with the Wraith, we added a team of specialist to add weapons and defensive capabilities."

"What are you saying?" Woolsey inquired.

"We have three ships almost fully operational."

"Elizabeth, I am totally one hundred percent sorry," Beckett pleaded as he approached his new patient who was sitting up on a diagnostic bed. "Please forgive me."

Elizabeth looked at him, puzzled. "Forgive you? Carson, what could you have possibly done that would warrant forgiveness?"

"I doubted you."

She paused. Finally, she offered him a half smile. "You're not the only one who has doubts. I'm afraid I can't forgive you because there's nothing to forgive." She regarded him. "You have discovered something?"

"Yes, I hav. I've discovered that you're not a clone or a replicator. You're not an alien shapeshifter or anything else like that." He smiled. "You're the genuine article, Elizabeth. You are flesh and blood. You have quite literally come back from the dead."

Elizabeth remained silent. She had no idea what to say.

He placed his hand on her arm. "Welcome back, Elizabeth."

"Thank you, Carson." She swallowed, trying to keep back her tears of gratitude. "I wasn't sure myself. I mean...how is this even possible?"

"You don't remember how you came to be here?"

She sighed. "I remember floating in space. Then...I woke up lying on a table in a lab." She shook her head and shrugged helplessly. "I don't remember anything else in between that."

Beckett paused in thought. "It's almost been a year since you led the replicators through the stargate, Elizabeth. I think there's only one explanation here. Much like what happened to Dr. Jackson, you must have ascended. Then, you must have done something taboo and they sent you back."

"If that is what happened, I don't remember any of it."

"Perhaps in time, you will. For now, let's go tell the others that you're back. Shall we?"

Elizabeth nodded as she got off the diagnostic bed.

Teyla and Ronon had taken the Athenians for a tour of the city and Patricia went to take care of a private matter while Woolsey, Johanson and Sheppard went to Woolsey's office. They had other things to discuss. Particularly, they had a matter to bring up that they didn't want to share with their guests.

"What do we do about Todd?" Sheppard asked no one in particular as he took a seat.

Johanson, always the Devil's Advocate, had an answer. "Why not just kill him? Why bother keeping him around? He's no good to us. He has nothing to offer."

Woolsey idly picked up a small statue of General George Hammond from his desk, wondering where it had come from and why he even had such a thing. Throughout all that had happened, he had forgotten that Carter had beamed it into his office just before Atlantis left earth. "I beg to differ." He placed the statue on the bookshelf before he turned to face Sheppard and Johanson. "I believe Todd has a lot to offer."

"You have something in mind?" Sheppard inquired, watching Woolsey curiously.

Woolsey leaned back onto his desk and folded his arms in front of him. "Yes, I do. Once the stargate is fully operational, I intend to let him go."

Johanson blinked. "What? Are you out of your mind?"

Sheppard sat up. "I'd hate to agree with Mr. Big Bird here, but I've got to say...That's a bad idea."

"Is it?" Woolsey paused. "I realize he's not exactly trustworthy, but I think it's something we should consider. We let him go under the condition that he owes us one in the future. That way at least we know he's out there and we might be able to use him to our advantage when the time comes. Plus, we don't know what's going on out there and he may be able to gather information for us."

"You're kidding, right?"

"You know I'm not kidding."

Johanson scowled. "Are you seriously thinking about letting that freak go? If you do that, Woolsey, my people will hear about it and we won't let your neglect of duty to Atlantis go unpunished."

Sheppard glared at him. "Oh, what the hell are you going to do? Talk him to death?" He shook his head. "You know what, I think we should let Todd go. I'll escort him to the stargate myself."

"You're making a big mistake."

"We'll send you with him. I'm sure he probably could use a snack right about now."

Johanson glared at him. Then, he turned his glare to Woolsey. "You haven't heard the last of this matter." He abruptly turned and stormed out of the office.

Sheppard shook his head. "He gets on my nerves, but that was fun."

"Actually," Woolsey agreed, "that was. But...Mr. Big Bird?"

Sheppard shrugged. "Something I heard General O' Neill call him. So...are we really doing this? Are we letting Todd go?"

"I believe it's the best option for us. He may prove more useful to us alive than if we kill him, which you know we won't do. We are not executioners under any circumstance."

Sheppard hesitated. "Well...maybe not today anyway. Look, I'll go talk to him and let him know he'll be able to leave soon." He nodded once and headed for the door.

"Colonel..."

Sheppard turned. "Yeah?"

"After that, why don't you head to Troye with Dr. McKay and his team? I'm sure you'll want to see these ships we were told about."

"Sure. I'll take Ronon. Maybe he can check out the soldiers. Give a few pointers. In fact, Teyla could, too."

"Teyla has already requested to remain here until we can link to New Athens through the stargate. She is anxious to learn of their fate. They could be casualties of war for all we know."

"Yeah. Look, I'll check those ships out but you've got to let me know once the stargate is operational."

Woolsey nodded. "I will."

"Thanks." With that, Sheppard left Woolsey's office feeling better now that there were several plans in motion. Things were beginning to come together.

Zelenka thought he was getting somewhere in Janus' lab. He was able to find a link from the lab on Atlantis and the lab under the City of Troye. It seemed to be a permanent link and made stronger by close proximity. He felt confident that answers would be forthcoming soon.

In fact, he discovered another computer link that suddenly came to life.

"Hello," he said, sitting up and looking at his laptop.

"Hello," Tony responded from his workstation.

Kate waved from her station. "Hi."

Zelenka frowned. "What? Stop that. I wasn't talking to either one of you."

"You said 'hello'," Tony pointed out.

Kate shrugged. "We just had to say 'hi' back."

"I was saying 'hello' to the discovery I just made." Zelenka tapped the keys on his keyboard, looking at the monitor intently. "There's another link to this lab...coming from somewhere..." He trailed off.

"Yeah, we know." Tony chuckled. "The link is Janus' second lab under Troye."

Zelenka slowly shook his head. "No...there is a third link and that third link leads to another place."

Kate looked at him, eyes wide with curiosity. "What other place, Dr. Zelenka? Where is it?"

"Somewhere far below us."

_ _  
>_ 4 _<p>

"Hello, Sheppard," Todd replied casually as he stood in the center of his cell. A half smile played across his face as he watched Sheppard enter his cell. "It is so wonderful to see you again after all this time."

Sheppard stopped and looked at him suspiciously. "Did you get a hair cut? You look...different."

"Perhaps it's all the sitting around I do since my incarceration. There is, after all, no other activities for me to do other than wait." He ignored the guards behind Sheppard. "Tell me, Sheppard...Is the wait over?"

Sheppard shrugged. "Yeah. Sure. Soon enough...you'll be on your way and out of my hair."

"If you don't like me in your hair, than perhaps it is you who should get a hair cut."

"Now that was just downright disturbing."

Todd paused as he regarded his visitor. "Not that I have any reason to doubt your word, Sheppard, but why should I believe you would release me back into the Pegasus Galaxy?"

"What makes you think we're in the Pegasus Galaxy?"

Todd looked insulted. "Oh, Sheppard. It is written all over your face. Besides, I can feel it. We are home. Where we belong. And I imagine you would release me so that we could continue our alliance, which is so full of trust for one another." He was, of course, being sarcastic.

"You know I'd rather put a bullet in you instead." Sheppard paused. "Several of them, in fact, just to be sure. But...Woolsey seems to think that letting you go is our best option." He narrowed his eyes as he looked at the Wraith before him. "What do you think? Is it our best option?"

"Well, as I understand our relationship, I would expect that you would want something in return for releasing me."

"What could you give in return, Todd?"

"I could find out what's been happening between my people and yours while you've been away."

Sheppard shrugged. "We probably could find out enough on our own."

Todd smiled. "I do have formidable resources to call upon."

"If you still have those resources."

Todd let out a laugh. "Sheppard, why toy with me? We both know the decision to release me has already been made. But if it should make you feel any better, I promise...As soon as I have any information that would benefit you, I will get it to you as soon as possible."

"Gee, thanks. That would be so swell of you." Sheppard glared at him. "You know if you try anything, I'll kill you."

"I wouldn't dream of it otherwise."

Sheppard paused as he regarded Todd. Finally, he shook his head. "I can't put my finger on it, but there is something different about you. I suppose it doesn't matter. You'll be gone by the end of the day."

"I miss your company already."

Sheppard just shook his head and left him. He had other matters to attend to so by the time he was far enough away from the cell to his liking, he had already pushed the Wraith from his thoughts.

Zelenka followed the link as best as he was able to on his personal laptop. It wasn't as difficult as he had thought it would have been. Once the program had opened back on earth from Janus' computers, it made whoever found it easy to follow and trace. That _whoever_ simply turned out to be Zelenka. He was grateful for the opportunity, especially when McKay was going to Troye. Basically that meant that he was in charge while McKay was away.

Woolsey looked at the monitor and viewed the work that Zelenka had been doing. "Are you saying that Janus has another hidden room here in Atlantis?"

Zelenka shrugged and pointed at the monitor. "That's what it looks like."

"Is it another lab?"

"Well, it really could be nothing more than sleeping quarters. Could lead to his own private room for all we know. We won't know for certain until we find it."

Woolsey paused in thought. "Where is it located?"

"According to this, somewhere directly below us. Far below. However, according to the schematics, there's no indication of any room so we can't say exactly where it's located." He sat back and nodded with determination. "But we'll find it."

"Excellent work, Dr. Zelenka. Inform me the second you do."

"I will."

Woolsey nodded his appreciation and headed out of Janus' lab.

Mace and Staci had been graciously invited to stay longer in Atlantis city, so they offered Sheppard the opportunity to fly the luxury jumper. The inside was wider and could easily seat eight people in the cockpit. The back was bigger as well with more room for supplies. Sheppard felt like a kid in a candy store although he tried hard not to show it. He took his seat and made preparations as McKay, three other scientists who were a part of McKay's team, and Ronon found seats for themselves.

"This is one sweet ride, eh, Sheppard?" Ronon replied, knowing that Sheppard himself wanted to admit it out loud.

Sheppard shrugged as if it didn't matter to him. "It's okay. I've been in better."

McKay snorted. "Since when?"

"What do you mean, since when? I've been at the helm of a ship of the Ancestors. You can't get any sweeter than that, although that ship was a little rusty."

"Well, this one isn't rusty."

Sheppard guided the jumper out of the bay and into the skies. "Okay...I've been directed to take us to their jumper bay where we'll be meeting some people. There'll be a representative from each department. Ronon, you're going with Marc Shiva. He'll take you to see the army they're talking about. Just watch yourself. I still don't trust these people."

"Who am I meeting?" McKay asked.

"Her name is Erin Greye. She'll take you and your team to the lab under Troye. Get your answers as quick as you can. If we need to pull out of here in a hurry, I'd like to be able to do it without having control of Atlantis being taken from us again."

McKay nodded. "Sure. Wait...I'm meeting a woman?"

"Yeah. Do you really have a problem with that?"

He shook his head quickly. "No, no, no, no. Just getting my facts right. That's all."

Ronon grinned. "I'll bet you're just wondering if you'll get a chance to see this Erin Greye naked."

McKay was horrified. "That is absolutely not true! It's also ridiculous! I don't want to see anyone naked!"

"That's too late for Dr. Weir."

"Come on! That wasn't even a long look! It was dark and I wasn't even sure what I was looking at!"

"Dr. McKay saw Elizabeth Weir naked?" one of McKay's scientist's asked.

Ronon nodded, grinning. "Yep."

"I did not!" McKay exclaimed. "I mean, come on, already! It was just a small peek."

"Alright, knock it off, you two." Sheppard shook his head and glanced at Ronon. "You're never going to let him forget that, are you?"

Ronon shook his head, still grinning. "Nope."

"Yeah, well...right now, we've got a mission to do, so let's do it and be quick about it. I'd like all of us to head back in a few hours and compare notes."

"You really believe these people aren't who they say they are?" Mckay asked.

"And you do?"

"They haven't done anything to make us _not_ trust them."

"McKay, they hijacked us from earth."

"They say they didn't."

"I don't believe them."

"Think about it, Sheppard. This just didn't happen randomly. It all happened from Janus' lab. Actually, it happened in each one of Janus' secret labs."

Sheppard frowned. "You actually think that Janus set this in motion?"

"I do."

"But why? If Janus is really behind this, why would he do it?"

McKay shrugged. "Maybe it was an assurance for him, knowing that he could keep Atlantis in the Pegasus Galaxy."

"Okay, that almost makes sense. But how do you explain...that _woman's_ appearance at the same time we're being hijacked on earth? Is Janus responsible for that, too?"

Mckay paused. "I don't know. Okay, so I don't have everything figured out yet! But I will."

"You'd better. As soon as we know what we're dealing with, we'll be able to come up with a plan...and I have to tell you, I love good planning."

"Welcome back, Dr. Weir," Woolsey greeted warmly as he gestured for her to have a seat in his office. "Elizabeth."

Elizabeth sat down and looked around her old office, an office that was no longer hers. "Thank you." She hesitated. "I'm so glad to be back, but...everything is so different. Even many of..." She wanted to say friends. "...the people have changed."

"A lot has changed in a year's time."

"You seem to be doing an excellent job of running Atlantis, Richard. I hope those at home realize that."

Woolsey shrugged. "If Johanson has his way, he would see to it that my reputation would be tarnished."

"From the IOA, that's to be expected."

He nodded. "So..." he began, changing the subject. "You are really Elizabeth Weir."

She nodded. "I am."

"Dr. Beckett tells me you don't remember how you got here."

She shrugged helplessly. "I don't."

"He also seems to think that the same thing which has happened to Dr. Jackson of SG-1 several years ago may have also happened to you. Do you think this is what happened to you?"

She shrugged again. "I'm not really sure if it is what happened to me or not. But...it does seem likely. Doesn't it?"

"You do realize that we must inform the SGC of your return as soon as we're able to. I'm sure they'll want you to go back for a full debriefing and see for themselves."

"How close are you to re-establishing contact with earth?" she asked.

He sat back. "I would like to say not long. We wanted to come back, but our return to Pegasus was rather hurried. We were unprepared, so doing things around here may take longer than usual." He paused. "Elizabeth...what do you know about the Athenians?"

She considered her answer before speaking. "I know as much about them as you do...but I do know that you can trust them."

"How do you know?"

"I just do."

He regarded her. "Until we can contact the SGC, could you act as an Ambassador between ourselves and the Athenians? We know they already like you, so they seem to accept you."

She nodded. "Yes. Of course. I'd be happy to."

"Thank you."

"You're welcome." Elizabeth was glad to help, but she couldn't help wondering if this office would ever be hers again.

Zelenka, Tony and Kate all heard the wooshing sound and they turned to look in the direction from whence it came. Slowly, Zelenka got up from his chair, glancing at the monitor on his laptop as he did so. Leaving his laptop, he moved toward the far wall, stopped in front of it and slowly pushed up his glasses with his middle finger.

"Huh," he said.

Tony and Kate joined him. Together, they saw that a section of the wall had moved aside, revealing a secret compartment. But not just any compartment. This compartment resembled something else.

"It's like one of the lifts," Tony said thoughtfully.

Zelenka nodded, looking at the schematics of the city on the monitor inside the compartment on the wall. "It does indeed."

"Couldn't it be just a closet?" Kate asked.

Zelenka shook his head. "I don't believe so." He moved back toward his workstation to retrieve his laptop. As he returned, he shook his head. "It's just as I suspected. Neither the room below us or this...closet, or even this lab are any where in the designs of Atlantis." He leaned into the compartment for a closer look. "However, the interior design of this closet is quite similar to any of the lifts we've been using here at Atlantis."

"If it's not a closet, why do you keep referring to it as one?"

Zelenka completely ignored the question.

So Kate asked a different one. "Can we get in and see where it takes us?"

"Let's not and say we did," Zelenka answered patiently.

"Well, it has to go to this other room, doesn't it?" Tony asked.

Zelenka shrugged. "In theory."

"Come on! Where else would it go?"

"Someplace flooded perhaps. You know that this city was never fully repaired since we've been here and for all we know, this could take us into a room full of water."

Kate frowned. "How are we going to find out?"

Zelenka paused. "I suppose we could place a camera on the floor and see if the lift floods when the door opens. if it floods...we'll know."

Tony headed for the door. "I'll go get a video cam!"

Sheppard parked in the jumper bay in Troye. He felt like he was inside a large parking garage, but the cleanest one he had ever seen. There were more luxury jumpers than he had ever seen.

The back door opened and everyone followed him out. There waiting for them were three Athenians. Two men and one woman. One of the men looked like a wrestler. _His arms are thicker than McKay's ego,_ Sheppard thought. The woman was hot, there was no mistake there. She had long blonde hair, blue eyes and nice long legs. However, Sheppard knew immediately that there was something completely odd about her...She couldn't take her eyes off McKay.

"Hi!" she practically exclaimed as she thrust her hand out to McKay. "You must be Dr. Rodney McKay! I've heard so much about you and I have to tell you what an opportunity this is for me."

Sheppard and Ronon exchanged looks.

Before the woman could say any more, Sheppard cleared his throat and introduced himself, Ronon, McKay and McKay's team of scientists. Then, he said, "We also are looking forward to this opportunity." _But I still don't trust you,_ he thought.

The wrestler-looking behemoth slapped his hand abruptly to his chest over his heart and then saluted. "Commander Marc Shiva," he said, introducing himself. "This is Dr. Erin Greye and Captain Al Berris. If there are no questions, we can begin the tours immediately."

Sheppard shrugged. "That's fine."

They split up. Ronon went with Shiva to a jumper. Sheppard joined Berris. And McKay and his team followed Erin to a jumper as she talked with excitement in her voice along the way. McKay couldn't jump into any type of conversation with her because she almost seemed not to stop talking even to take a breath.

Shiva and Ronon took a jumper, headed for the skies and flew toward the east. For a short time, they were both silent. Shiva concentrated on flying while Ronon watched the city passing below them.

Finally, Shiva broke the silence between them. "Do you have any questions?"

"Nope."

"You are here to observe and assess, are you not?"

"Yep."

Shiva paused. "What are you looking for in our army?"

Ronon shrugged. "Not much. If they can kill Wraith, that's all that matters."

The big Athenian nodded once. "I hate to admit it...but I am almost ashamed that we haven't done this sooner. When we first heard of Atlantis' rising, only then did we begin to prepare ourselves for war. But before that, all we knew was peace." He paused. "Your Colonel Sheppard does not trust us."

"What makes you say that?"

"I can see it in his eyes. The way he stands. As if at a second's notice, he will suddenly attack."

Ronon shrugged. "He has reservations. We all do."

"You do as well."

"Sure. It's hard to trust people who have been sheltered from the Wraith while everybody else out there is dying."

Shiva nodded slowly. "I...understand your reservations."

Ronon didn't say anything.

"It is my hope that you will like our army. They've been trained well...but they need to be trained by experienced warriors. Lenox and Groh have trained some during their visits, but we haven't seen them in quite some time." Suddenly, he smiled as he pointed out the window at something below them. "There."

Ronon looked and despite those reservations he shared with Sheppard, he couldn't help but be impressed. On the grounds below them, several platoons of men were training. Some were marching. Others were running. Some were facing each other in hand-to-hand combat maneuvers. All of it brought memories to Ronon of his own training.

"Everyone down there," he began, turning to look at the Commander. "They're doing this because they want to fight the Wraith?"

Shiva nodded. "With all of their might."

Ronon was impressed.

The gate was once again operational and with the new point of origin, New Athens was the first to be dialed. Teyla took a team with her to re-establish contact with her people. Woolsey was happy that something had gone right for them for a change. At the moment, however, he was not happy with Major Lorne's recent discovery.

They walked together, heading for Janus' lab.

"You're certain their nowhere to be found anywhere in the city?" Woolsey inquired.

Major Lorne shook his head grimly. "It's as if they vanished."

"How many are unaccounted for?"

"Six."

"And you're certain that they were all with us after we left earth?"

Lorne nodded. "According to several witnesses, yes."

Woolsey frowned. "Well, I can't say that I like this news at all. What could have happened to them? Where are they now?"

"We've used the internal sensors and haven't been able to locate them anywhere in the city. Our investigation reveals that they're just not here. Period."

Woolsey stopped walking. "Unless..."

Lorne stopped as well. "Unless...what?"

"Unless they're in an area of the city that our sensors can't penetrate."

"Where would that be?"

"Dr. Zelenka thinks he may have discovered another hidden room somewhere far below us. I'm heading to Janus' lab to check on his progress."

They arrived at the lab where Zelenka, Tony and Kate were watching a video on Zelenka's laptop.

"I don't think it's flooded," Kate was saying, "but it sure is dark down there."

Zelenka nodded in agreement.

"What are you looking at?" Woolsey inquired.

Zelenka glanced at him, noticing Lorne's presence. "We sent a video cam to the secret room, but can't tell what's in there because it's too dark. At least - as Kate has pointed out - it isn't flooded." He sat back. "I think it's time we go see for ourselves."

"Excellent. We arrived just in time then."

Zelenka moved toward the wall with his laptop. He keyed in a code and the wall opened up, revealing the transport chamber. He entered it with Woolsey and Lorne joining him. As if the chamber sensed their presence, it closed.

Woolsey looked around. Usually, there were obvious controls to operate, but in this transport chamber, there were no such controls present. "How do we operate this?" he asked.

Zelenka grinned. "The chamber itself doesn't exactly move."

"It doesn't?" Lorne asked.

"No." He entered another code into his laptop.

There was a bright flash. Then, nothing.

"What the hell was that?" Woolsey demanded.

"We were just transported," Zelenka assured him.

As if on queue, the chamber opened. The three men looked out into a very dark room.

Zelenka leaned into the room. As he did, light began to come to life, brightening the room. They stood there, stunned by what they saw. It was a lab, but it was bigger than any they had ever seen on Atlantis. It was bigger than the infirmary. There were four empty rooms to the right and four empty rooms to the left. What those rooms had been used for was anyone's guess. To the rear of the large open room, there was a sudden bang, followed by a deep hum. As they stared in awe, a large panel slid up and for the first time in a long while they were able to see the ocean just outside the city. A large snake-like beast swam by at an incredible rate of speed.

Woolsey swallowed. "Out of every expectation that I've had for what was down here...this wasn't one of them."

_ _  
>_ Epilogue _<p>

"Chuck, where is Mr. Woolsey?" Sheppard wanted to know as he entered the Control Room. His mind was still going over what he had seen hours ago in a private facility hundreds of miles out of Troye. By the time he had returned to Atlantis, a whole day had passed and he was exhausted.

However, tired or not, there was still plenty to do.

Chuck answered as he turned from his workstation. "Mr. Woolsey is in Janus' new secret lab with Dr. Zelenka."

Sheppard frowned. "Did you say there's a new secret lab?"

Chuck nodded. "I did."

"Oh, crap. Every time we find something like that, trouble soon follows. So McKay didn't make this discovery. It had to have been Radek."

"It was. They've been in there for most of the day. Mr. Woolsey doesn't recommend swimming out there in the ocean."

Sheppard shrugged. "Wasn't planning on it, but why not?"

"Something about giant snakes."

Sheppard paused. "Oh. Well, that's good to know. Anyway, that's all just great. But why is Mr. Woolsey still down there anyway? I thought administration was more his thing. Not science."

Chuck shrugged. "I don't really know. You should ask him."

"I'll do that. But first..." He adjusted his earpiece. "Major Lorne..."

_"Go ahead, Colonel,"_ came the quick response.

"Better go fetch Todd so we can get him on his way."

_"I'm on it. We're already on our way."_

Sheppard grimaced. "Great." He saw Johanson, Patricia and Doreen coming up the stairs and let out a sigh. Doreen didn't look happy at all, but she was IOA. None of them were ever happy unless every one else around them was miserable. "Swell," he muttered. "Look who's joining the party."

"Colonel," Johanson growled as he placed himself directly in front of Sheppard, "I strongly advise you to stop this course of action. Letting that monster go is a grave mistake."

Sheppard shrugged indifferently. "Yeah, well, I feel the same way about keeping you around, but that's out of my hands. Not that I haven't given it much thought, because I have. Soon as I come up with a solution to that, you'll be the first to know."

"I don't like your tone."

"I'm not really concerned with what you like or don't like. If you'll excuse me, I've got some more important matters to attend to."

"Colonel Carter, we're coming out of hyperdrive," Walter announced unnecessarily as the George Hammond traveled through space.

Samantha was standing in front of the large windows, watching the hyperdrive corridor stretch out before them. Suddenly, the view changed in an instant and they were out of hyperdrive. Space looked very large when the stars weren't whipping past at an alarming rate. It was full of stars.

She frowned.

That was the problem. All she saw were stars. There wasn't a planet in sight.

"That signal we were tracing..." She let out a sigh. "I don't understand. General O' Neill assured me that it would lead us straight to Atlantis. The natural assumption then would be that we would find Atlantis on a planet or possibly even adrift in space. But there's nothing here."

"There has to be something, Colonel," Walter told her.

"But there's nothing."

"There has to be. We're still getting the signal loud and clear." Walter looked up from his workstation. "They should be right in front of us."

Samantha squinted her eyes and tried to search for any sign of Atlantis or a planet...but there was nothing.

They dialed up a planet that Todd had mentioned to be a neutral location. He and Sheppard stood in front of the open stargate while behind them, Lorne and several marines stood by. They were prepared for anything.

Todd smiled wryly as he took in the wormhole at the center of the stargate. Slowly, he turned to face Sheppard. "So...this is good-bye."

Sheppard shrugged. "Until we meet again." He leaned forward. "Just remember what we talked about."

"I assure you, John Sheppard, anything you say to me is never something easily forgotten."

"Great. It's so nice to know you think about me. Believe me, I think of you all the time, too." He paused. "We've shared a very fragile alliance with each other for a long time."

Todd bowed his head in agreement. "Indeed, we have."

"We both know it's not going to last."

"What is that saying on your world, Sheppard?" He smiled. "All good things must come to an end."

"This has never been a good thing, but it will end."

"And when it does, you'll what? Kill me?"

Sheppard shrugged. "Maybe. I certainly won't rule it out."

"Perhaps it will be I who kills you." He smiled and leaned closer, as if to speak in confidence. "Or perhaps something most unexpected will happen. We might actually become...friends."

Sheppard narrowed his eyes. "You've overstayed your visit."

Todd continued to smile. He bowed his head once again, turned and stepped into the gate. Seconds later, the gate closed and Todd was finally gone.

"You just made a big mistake," Johanson said from the stairs, shaking his head in disgust.

Sheppard ignored him as he headed up the stairs back to the Control Room. As he did, Chuck was waiting for him. "Colonel, we've just made contact," Chuck informed him.

Sheppard stopped. "Contact? With who?"

Chuck pointed to his monitor.

Sheppard came around the workstation and was astonished to see the smiling face of Colonel Samantha Carter. "Son-of-a-bitch!" he exclaimed. "How did you find us?"

_"General O' Neill gave a gift to Mr. Woolsey just before you left,"_ Samantha told him.

He couldn't stop grinning. "You tracked us."

_"Yes, we did. Colonel Sheppard, we're here to help. However, it would help us if we could actually see you."_ She waved her hands, helpless. _"If you'll turn off the cloak, we'll be better able to assist you."_

"Sam...Atlantis isn't cloaked."

_"It isn't? How can that be? We can't see you."_ She shrugged. _"We can't see Atlantis at all."_

"Atlantis isn't cloaked...but the planet we're on _is._"

The look of astonishment on Samantha's face was priceless.

The silent observers in their black ship had completed their task. They had observed the arrival of the George Hammond. They considered that to be the signal for them to leave. They moved far out of range, opened a hyperspace window and disappeared into it.


End file.
